Bump the runtime-dependencies group across 1 directory with 8 updates

[dependabot]

Bumps the runtime-dependencies group with 8 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	2.2.1
pandas	2.2.2	2.2.3
pydantic	2.8.2	2.10.5
ruamel-yaml	0.18.6	0.18.10
scipy	1.14.1	1.15.0
sdtfile	2024.5.24	2024.12.6

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

• See full diff in compare view

Updates numpy from 2.0.1 to 2.2.1

Release notes

Sourced from numpy's releases.

2.2.1 (DEC 21, 2024)

NumPy 2.2.1 Release Notes

NumPy 2.2.1 is a patch release following 2.2.0. It fixes bugs found after the 2.2.0 release and has several maintenance pins to work around upstream changes.

There was some breakage in downstream projects following the 2.2.0 release due to updates to NumPy typing. Because of problems due to MyPy defects, we recommend using basedpyright for type checking, it can be installed from PyPI. The Pylance extension for Visual Studio Code is also based on Pyright. Problems that persist when using basedpyright should be reported as issues on the NumPy github site.

This release supports Python 3.10-3.13.

Contributors

A total of 9 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

• Charles Harris
• Joren Hammudoglu
• Matti Picus
• Nathan Goldbaum
• Peter Hawkins
• Simon Altrogge
• Thomas A Caswell
• Warren Weckesser
• Yang Wang +

Pull requests merged

A total of 12 pull requests were merged for this release.

• #27935: MAINT: Prepare 2.2.x for further development
• #27950: TEST: cleanups
• #27958: BUG: fix use-after-free error in npy_hashtable.cpp (#27955)
• #27959: BLD: add missing include
• #27982: BUG:fix compile error libatomic link test to meson.build
• #27990: TYP: Fix falsely rejected value types in ndarray.__setitem__
• #27991: MAINT: Don't wrap #include <Python.h> with extern "C"
• #27993: BUG: Fix segfault in stringdtype lexsort
• #28006: MAINT: random: Tweak module code in mtrand.pyx to fix a Cython...
• #28007: BUG: Cython API was missing NPY_UINTP.
• #28021: CI: pin scipy-doctest to 1.5.1
• #28044: TYP: allow None in operand sequence of nditer

Checksums

... (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

• 7469245 Merge pull request #28047 from charris/prepare-2.2.1
• acb051e REL: Prepare for the NumPy 2.2.1 release [wheel build]
• 28a091a Merge pull request #28044 from charris/backport-28039
• 723605b TST: Add test for allowing None in operand sequence passed to nditer
• 554739e TYP: allow None in operand sequence of nditer
• 31bc4c8 Merge pull request #28021 from charris/backport-28020
• 32f52a3 CI: pin scipy-doctest to 1.5.1 (#28020)
• 6219aeb Merge pull request #28007 from charris/backport-28005
• eb7071c Merge pull request #28006 from charris/backport-28003
• 4f82c32 BUG: Cython API was missing NPY_UINTP.
• 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

• 0691c5c RLS: 2.2.3
• 658dfdd relax cython bound
• 6891e90 Backport PR #59847: BLD: Build wheels for Python 3.13 on aarch64 as well
• f108468 RLS: 2.2.3
• 6958738 Backport PR #59840: BLD: Final release prep for 2.2.3 (#59842)
• 0bd98fe Backport PR #59136 on branch 2.2.x (Upload 3.13 & free-threaded nightly wheel...
• 8d67e77 Backport PR #59836 on branch 2.2.x (BLD: Fix bad Cython annotation) (#59837)
• f7b6378 Assorted backports for 2.2.x (#59785)
• 2127b42 Backport #59144 on 2.2.x / 2.3.x (remove ops div class to solve #2137) (#59535)
• 4a20adb Backport PR #59813 on branch 2.2.x (CI: Debug failing ARM builds) (#59828)
• Additional commits viewable in compare view

Updates pydantic from 2.8.2 to 2.10.5

Release notes

Sourced from pydantic's releases.

v2.10.5 2024-12-18

v2.10.5 (2025-01-08)

What's Changed

• Remove custom MRO implementation of Pydantic models by @​Viicos in #11184
• Fix URL serialization for unions by @​sydney-runkle in #11233

v2.10.4 2024-12-18

What's Changed

Packaging

• Bump pydantic-core to v2.27.2 by @​davidhewitt in #11138

Fixes

• Fix for comparison of AnyUrl objects by @​alexprabhat99 in #11082
• Properly fetch PEP 695 type params for functions, do not fetch annotations from signature by @​Viicos in #11093
• Include JSON Schema input core schema in function schemas by @​Viicos in #11085
• Add len to _BaseUrl to avoid TypeError by @​Kharianne in #11111
• Make sure the type reference is removed from the seen references by @​Viicos in #11143

New Contributors

• @​alexprabhat99 made their first contribution in #11082
• @​Kharianne made their first contribution in #11111

Full Changelog: pydantic/pydantic@v2.10.3...v2.10.4

v2.10.3 2024-12-03

What's Changed

Fixes

• Set fields when defer_build is set on Pydantic dataclasses by @​Viicos in #10984
• Do not resolve the JSON Schema reference for dict core schema keys by @​Viicos in #10989
• Use the globals of the function when evaluating the return type for PlainSerializer and WrapSerializer functions by @​Viicos in #11008
• Fix host required enforcement for urls to be compatible with v2.9 behavior by @​sydney-runkle in #11027
• Add a default_factory_takes_validated_data property to FieldInfo by @​Viicos in #11034
• Fix url json schema in serialization mode by @​sydney-runkle in #11035

Full Changelog: pydantic/pydantic@v2.10.2...v2.10.3

v2.10.2 2024-11-26

What's Changed

Fixes

• Only evaluate FieldInfo annotations if required during schema building by @​Viicos in #10769

... (truncated)

Changelog

Sourced from pydantic's changelog.

v2.10.5 (2025-01-08)

GitHub release

What's Changed

• Remove custom MRO implementation of Pydantic models by @​Viicos in #11184
• Fix URL serialization for unions by @​sydney-runkle in #11233

v2.10.4 (2024-12-18)

GitHub release

What's Changed

Packaging

• Bump pydantic-core to v2.27.2 by @​davidhewitt in #11138

Fixes

• Fix for comparison of AnyUrl objects by @​alexprabhat99 in #11082
• Properly fetch PEP 695 type params for functions, do not fetch annotations from signature by @​Viicos in #11093
• Include JSON Schema input core schema in function schemas by @​Viicos in #11085
• Add len to _BaseUrl to avoid TypeError by @​Kharianne in #11111
• Make sure the type reference is removed from the seen references by @​Viicos in #11143

New Contributors

• @​FyZzyss made their first contribution in #10789
• @​tamird made their first contribution in #10948
• @​felixxm made their first contribution in #11077
• @​alexprabhat99 made their first contribution in #11082
• @​Kharianne made their first contribution in #11111

v2.10.3 (2024-12-03)

GitHub release

What's Changed

Fixes

• Set fields when defer_build is set on Pydantic dataclasses by @​Viicos in #10984
• Do not resolve the JSON Schema reference for dict core schema keys by @​Viicos in #10989
• Use the globals of the function when evaluating the return type for PlainSerializer and WrapSerializer functions by @​Viicos in #11008
• Fix host required enforcement for urls to be compatible with v2.9 behavior by @​sydney-runkle in #11027
• Add a default_factory_takes_validated_data property to FieldInfo by @​Viicos in #11034
• Fix url json schema in serialization mode by @​sydney-runkle in #11035

... (truncated)

Commits

• 5d34efd Prepare release v2.10.5 (#11237)
• 6e585f9 Fix url serialization for unions (#11233)
• 5a22e02 Remove custom MRO implementation of Pydantic models (#11195)
• 5bd3a65 fix history.md
• 46f0945 Prepare for v2.10.4 (#11144)
• ea69e69 Make sure the type reference is removed from the seen references (#11145)
• a07c31e Include JSON Schema input core schema in function schemas (#11142)
• 9166d55 Update WithJsonSchema documentation, add usage documentation for `json_sche...
• 572f57d Rewrite validators documentation (#11060)
• 9faa8d9 Fix for comaparison of AnyUrl objects (#11082)
• Additional commits viewable in compare view

Updates ruamel-yaml from 0.18.6 to 0.18.10

Updates scipy from 1.14.1 to 1.15.0

Release notes

Sourced from scipy's releases.

SciPy 1.15.0 Release Notes

SciPy 1.15.0 is the culmination of 6 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 1.15.x branch, and on adding new features on the main branch.

This release requires Python 3.10-3.13 and NumPy 1.23.5 or greater.

Highlights of this release

• Sparse arrays are now fully functional for 1-D and 2-D arrays. We recommend that all new code use sparse arrays instead of sparse matrices and that developers start to migrate their existing code from sparse matrix to sparse array: migration_to_sparray. Both sparse.linalg and sparse.csgraph work with either sparse matrix or sparse array and work internally with sparse array.

• Sparse arrays now provide basic support for n-D arrays in the COO format including add, subtract, reshape, transpose, matmul, dot, tensordot and others. More functionality is coming in future releases.

• Preliminary support for free-threaded Python 3.13.

• New probability distribution features in scipy.stats can be used to improve the speed and accuracy of existing continuous distributions and perform new probability calculations.

• Several new features support vectorized calculations with Python Array API Standard compatible input (see "Array API Standard Support" below):

  • scipy.differentiate is a new top-level submodule for accurate estimation of derivatives of black box functions.
  • scipy.optimize.elementwise contains new functions for root-finding and minimization of univariate functions.
  • scipy.integrate offers new functions cubature, tanhsinh, and nsum for multivariate integration, univariate integration, and univariate series summation, respectively.

• scipy.interpolate.AAA adds the AAA algorithm for barycentric rational approximation of real or complex functions.

• scipy.special adds new functions offering improved Legendre function implementations with a more consistent interface.

... (truncated)

Commits

• 6e246d0 REL: 1.15.0 "final" rel commit [wheel build]
• ed7c850 Merge pull request #22233 from tylerjereddy/treddy_backports_1.15.0_final
• 2e2f2cd MAINT: PR 22233 wheel build [wheel build]
• f05c622 DOC: Update 1.15.0 relnotes
• 7348d92 Update scipy/differentiate/_differentiate.py
• 56b1f7e DOC: differentiate.jacobian: correct/improve documentation about callable int...
• 30077e7 DEP: linalg.solve_toeplitz/matmul_toeplitz: warn on n-D c, r (#22193)
• 256c1a2 Merge pull request #22181 from tylerjereddy/treddy_prep_scipy_1.15.0rc3
• f046276 REL: set 1.15.0rc3 unreleased
• a3d40a8 REL: 1.15.0rc2 rel commit [wheel build]
• Additional commits viewable in compare view

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

• 96afd12 Release v2024.12.6
• bd6f037 Update CHANGES.rst
• 3ec4a2c Update sdtfile/sdtfile.py
• bc66e0e Release v2024.11.24
• 243c910 Update CHANGES.rst
• 544573f Update setup.py
• 26a4e0c Update sdtfile/sdtfile.py
• e4ebe26 Update sdtfile/init.py
• See full diff in compare view

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Summary by Sourcery

Build:

• Update numpy dependency constraint to <2.3

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request updates the runtime dependencies for several packages.

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

File-Level Changes

Change	Details	Files
Update asteval from 1.0.2 to 1.0.5	Improved error management and exception handling. Added support for deleting subscripts. Nested symbol tables now have a Group() function. Functions defined within asteval now have a _signature() method, used in repr. Non-boolean return values from comparison operators now behave like Python, not immediately testing as bool.	pyproject.toml requirements_pinned.txt
Update netcdf4 from 1.7.1.post1 to 1.7.2	Added static type hints. Exposed nc_rc_set and nc_rc_get via module functions. Added Variable.get_fill_value and allowed fill_value='default'. Fixed NETCDF3 endian error. Support os.PathLike arguments for Dataset.fromcdl and raise FileNotFoundError or FileExistsError if appropriate. Raise more informative error when trying to iterate or perform a membership operation on a Dataset. Fixed type hint for createEnumType. Added Python 3.13 to Windows wheel builds.	pyproject.toml requirements_pinned.txt
Update numpy from 2.0.1 to 2.2.1	Fixed a use-after-free error in npy_hashtable.cpp. Fixed falsely rejected value types in ndarray.setitem. Fixed segfault in stringdtype lexsort. Fixed a Cython incompatibility in mtrand.pyx. Added a missing NPY_UINTP to the Cython API. Pinned scipy-doctest to 1.5.1 in CI. Allowed None in the operand sequence of nditer.	pyproject.toml requirements_pinned.txt
Update pandas from 2.2.2 to 2.2.3	Built wheels for Python 3.13 on aarch64. Fixed a bad Cython annotation. Removed ops div class to solve #2137. Debugged failing ARM builds.	pyproject.toml requirements_pinned.txt
Update pydantic from 2.8.2 to 2.10.5	Removed custom MRO implementation of Pydantic models. Fixed URL serialization for unions. Bumped pydantic-core to v2.27.2. Fixed comparison of AnyUrl objects. Fixed PEP 695 type params fetching for functions. Included JSON Schema input core schema in function schemas. Added len to _BaseUrl to avoid TypeError. Ensured type reference removal from seen references. Set fields when defer_build is set on Pydantic dataclasses. Fixed JSON Schema reference resolution for dict core schema keys. Used function globals when evaluating return type for PlainSerializer and WrapSerializer functions. Fixed host required enforcement for URLs to be compatible with v2.9 behavior. Added default_factory_takes_validated_data property to FieldInfo. Fixed URL JSON schema in serialization mode.	pyproject.toml requirements_pinned.txt
Update ruamel-yaml from 0.18.6 to 0.18.10		pyproject.toml requirements_pinned.txt
Update scipy from 1.14.1 to 1.15.0	Sparse arrays are now fully functional for 1-D and 2-D arrays. Preliminary support for free-threaded Python 3.13. New probability distribution features in scipy.stats. Several new features support vectorized calculations with Python Array API Standard compatible input. Added scipy.differentiate submodule for accurate estimation of derivatives. Added new functions to scipy.optimize.elementwise for root-finding and minimization. Added new functions to scipy.integrate for multivariate and univariate integration and series summation. Added AAA algorithm to scipy.interpolate for barycentric rational approximation. Added new functions to scipy.special for improved Legendre function implementations.	pyproject.toml requirements_pinned.txt
Update sdtfile from 2024.5.24 to 2024.12.6	Fixed reading MeasureInfo fields as scalars. Updated some structure field names with BH reference. Parsed some SetupBlock binary structures. Included more information in str(SdtFile). Added subtype to FileRevision. Updated MEASURE_INFO_EXT struct to SPCM v.9.9.	pyproject.toml requirements_pinned.txt

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👈 Launch a binder notebook on branch glotaran/pyglotaran/dependabot/pip/staging/runtime-dependencies-7df8d10622

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