Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Bump the runtime-dependencies group across 1 directory with 9 updates #1580

Open
wants to merge 2 commits into
base: staging
Choose a base branch
from

Conversation

dependabot[bot]
Copy link
Contributor

@dependabot dependabot bot commented on behalf of github Feb 21, 2025

Bumps the runtime-dependencies group with 9 updates in the / directory:

Package From To
asteval 1.0.2 1.0.6
netcdf4 1.7.1.post1 1.7.2
numba 0.60.0 0.61.0
numpy 2.0.1 2.2.3
pandas 2.2.2 2.2.3
pydantic 2.8.2 2.10.6
ruamel-yaml 0.18.6 0.18.10
scipy 1.14.1 1.15.2
sdtfile 2024.5.24 2024.12.6

Updates asteval from 1.0.2 to 1.0.6

Release notes

Sourced from asteval's releases.

1.0.6

  • drop testing and support for Python3.8, add Python 3.13, change document to reflect this.
  • implement safe_getattr and safe_format functions; fix bugs in UNSAFE_ATTRS and UNSAFE_ATTRS_DTYPES usage
  • make all procedure attributes private to curb access to AST nodes, which can be exploited
  • improvements to error messages, including use ast functions to construct better error messages
  • remove import of numpy.linalg, as documented
  • update doc description for security advisory

Special thanks to @​SteakEnthusiast for the security-related fixes

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
  • 40c3196 document support for Python 3.9 to 3.13
  • 70eb46b using ast functions to construct better error messages
  • b578ce1 work on improving error messages
  • 9dbd8ad update supported version
  • ea78397 update copyright
  • 36abc02 change tested versions to 3.9 to 3.13
  • 68a43a1 drop Python3.8 testing
  • 8e0700e include text and better lineno info for better exceptions
  • 6970d89 some doc updates
  • 5840a7f fix doc Makefile
  • 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 numba from 0.60.0 to 0.61.0

Release notes

Sourced from numba's releases.

Numba 0.61.0

Major Numba release adding Python 3.13 and NumPy 2.1 support. View detailed release notes and changelog here.

Commits
  • 8ec16ce Merge pull request #9897 from kc611/release0.61
  • a9ee23a Fixed NumPy versioning issue in RTD
  • 01e0bcd Updated version support table
  • 0ae7143 Modified changelog for 0.61.0 final
  • 7d23618 Merge pull request #9887 from sklam/misc/disable_coverage
  • 0d7b433 Merge pull request #9843 from kc611/release0.61
  • 3735191 Update docs/source/release/0.61.0-notes.rst
  • 1bd3d0f Updated changelog entries
  • d74d94e Merge pull request #9848 from sklam/fix/py3_13_1_getiter
  • bf20b30 Added Changlog entries for RC2
  • Additional commits viewable in compare view

Updates numpy from 2.0.1 to 2.2.3

Release notes

Sourced from numpy's releases.

2.2.3 (Feb 13, 2025)

NumPy 2.2.3 Release Notes

NumPy 2.2.3 is a patch release that fixes bugs found after the 2.2.2 release. The majority of the changes are typing improvements and fixes for free threaded Python. Both of those areas are still under development, so if you discover new problems, please report them.

This release supports Python versions 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.

  • !amotzop
  • Charles Harris
  • Chris Sidebottom
  • Joren Hammudoglu
  • Matthew Brett
  • Nathan Goldbaum
  • Raghuveer Devulapalli
  • Sebastian Berg
  • Yakov Danishevsky +

Pull requests merged

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

  • #28185: MAINT: Prepare 2.2.x for further development
  • #28201: BUG: fix data race in a more minimal way on stable branch
  • #28208: BUG: Fix from_float_positional errors for huge pads
  • #28209: BUG: fix data race in np.repeat
  • #28212: MAINT: Use VQSORT_COMPILER_COMPATIBLE to determine if we should...
  • #28224: MAINT: update highway to latest
  • #28236: BUG: Add cpp atomic support (#28234)
  • #28237: BLD: Compile fix for clang-cl on WoA
  • #28243: TYP: Avoid upcasting float64 in the set-ops
  • #28249: BLD: better fix for clang / ARM compiles
  • #28266: TYP: Fix timedelta64.__divmod__ and timedelta64.__mod__...
  • #28274: TYP: Fixed missing typing information of set_printoptions
  • #28278: BUG: backport resource cleanup bugfix from gh-28273
  • #28282: BUG: fix incorrect bytes to stringdtype coercion
  • #28283: TYP: Fix scalar constructors
  • #28284: TYP: stub numpy.matlib
  • #28285: TYP: stub the missing numpy.testing modules
  • #28286: CI: Fix the github label for TYP: PR's and issues
  • #28305: TYP: Backport typing updates from main
  • #28321: BUG: fix race initializing legacy dtype casts
  • #28324: CI: update test_moderately_small_alpha

... (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
  • a274561 Merge pull request #28322 from charris/prepare-2.2.3
  • 5ab0f71 REL: Prepare for the NumPy 2.2.3 release [wheel build]
  • 010ad9b Merge pull request #28324 from charris/update-test_dirichlet_moderately_small...
  • 6338746 CI: update test_moderately_small_alpha [wheel build]
  • 56f8d5b Merge pull request #28321 from charris/backport-28290
  • 48515a3 MAINT: Update some testing files from main
  • 96ca7e3 MAINT: respond to code review
  • c20ac88 MAINT: use a try/finally to make the deadlock protection more robust
  • d494647 MAINT: fix indentation and clarify comment
  • 3f8fbd6 MAINT: go back to try/except
  • 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 2.10.6

Release notes

Sourced from pydantic's releases.

v2.10.6 2025-01-23

What's Changed

Fixes

Full Changelog: pydantic/pydantic@v2.10.5...v2.10.6

v2.10.5 2024-12-18

What's Changed

Fixes

Full Changelog: pydantic/pydantic@v2.10.4...v2.10.5

v2.10.4 2024-12-18

What's Changed

Packaging

Fixes

New Contributors

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

... (truncated)

Changelog

Sourced from pydantic's changelog.

v2.10.6 (2025-01-23)

GitHub release

What's Changed

Fixes

v2.10.5 (2025-01-08)

GitHub release

What's Changed

Fixes

v2.10.4 (2024-12-18)

GitHub release

What's Changed

Packaging

Fixes

New Contributors

v2.10.3 (2024-12-03)

... (truncated)

Commits

Updates ruamel-yaml from 0.18.6 to 0.18.10

Updates scipy from 1.14.1 to 1.15.2

Release notes

Sourced from scipy's releases.

SciPy 1.15.2 Release Notes

SciPy 1.15.2 is a bug-fix release with no new features compared to 1.15.1. Free-threaded Python 3.13 wheels for Linux ARM platform are available on PyPI starting with this release.

Authors

  • Name (commits)
  • Peter Bell (1)
  • Charles Bousseau (1) +
  • Jake Bowhay (3)
  • Matthew Brett (1)
  • Ralf Gommers (3)
  • Rohit Goswami (1)
  • Matt Haberland (4)
  • Parth Nobel (1) +
  • Tyler Reddy (33)
  • Daniel Schmitz (2)
  • Dan Schult (5)
  • Scott Shambaugh (2)
  • Edgar Andrés Margffoy Tuay (1)
  • Warren Weckesser (4)

A total of 14 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 1.15.1 Release Notes

SciPy 1.15.1 is a bug-fix release with no new features compared to 1.15.0. Importantly, an issue with the import of scipy.optimize breaking other packages has been fixed.

Authors

  • Name (commits)
  • Ralf Gommers (3)
  • Rohit Goswami (1)
  • Matt Haberland (2)
  • Tyler Reddy (7)
  • Daniel Schmitz (1)

... (truncated)

Commits
  • 0f1fd4a REL: 1.15.2 rel commit [wheel build]
  • 7df5cc6 Merge pull request #22471 from tylerjereddy/treddy_backports_1.15.2
  • a046fa0 CI: PR 22471 wheel builds [wheel build]
  • 198aa52 DOC: PR 22471 revisions
  • ba61a58 CI: PR 22471 revisions
  • e0251ee do not check dtype in test_compare_with_GCVSPL
  • fcc68dd MAINT: integrate.cumulative_simpson: bump test tolerance
  • 6d2c059 BUG: wrap median_filter stability (#22402)
  • 59cb7d4 DOC: PR 22471 revisions
  • a60d17f MAINT: pearsonr SIMD-related shim
  • 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

You can trigger a rebase of this PR 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

Summary by Sourcery

This pull request updates the runtime dependencies to the latest versions.

Enhancements:

  • Update the upper bound of the numpy dependency to <2.3.

Chores:

  • Bump the runtime-dependencies group, including updates to asteval, netcdf4, numba, numpy, pandas, pydantic, ruamel-yaml, scipy, and sdtfile.

Bumps the runtime-dependencies group with 9 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| [asteval](/~https://github.com/lmfit/asteval) | `1.0.2` | `1.0.6` |
| [netcdf4](/~https://github.com/Unidata/netcdf4-python) | `1.7.1.post1` | `1.7.2` |
| [numba](/~https://github.com/numba/numba) | `0.60.0` | `0.61.0` |
| [numpy](/~https://github.com/numpy/numpy) | `2.0.1` | `2.2.3` |
| [pandas](/~https://github.com/pandas-dev/pandas) | `2.2.2` | `2.2.3` |
| [pydantic](/~https://github.com/pydantic/pydantic) | `2.8.2` | `2.10.6` |
| ruamel-yaml | `0.18.6` | `0.18.10` |
| [scipy](/~https://github.com/scipy/scipy) | `1.14.1` | `1.15.2` |
| [sdtfile](/~https://github.com/cgohlke/sdtfile) | `2024.5.24` | `2024.12.6` |



Updates `asteval` from 1.0.2 to 1.0.6
- [Release notes](/~https://github.com/lmfit/asteval/releases)
- [Commits](lmfit/asteval@1.0.2...1.0.6)

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 `numba` from 0.60.0 to 0.61.0
- [Release notes](/~https://github.com/numba/numba/releases)
- [Commits](numba/numba@0.60.0...0.61.0)

Updates `numpy` from 2.0.1 to 2.2.3
- [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...v2.2.3)

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 2.10.6
- [Release notes](/~https://github.com/pydantic/pydantic/releases)
- [Changelog](/~https://github.com/pydantic/pydantic/blob/main/HISTORY.md)
- [Commits](pydantic/pydantic@v2.8.2...v2.10.6)

Updates `ruamel-yaml` from 0.18.6 to 0.18.10

Updates `scipy` from 1.14.1 to 1.15.2
- [Release notes](/~https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.14.1...v1.15.2)

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)

---
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: numba
  dependency-type: direct:production
  update-type: version-update:semver-minor
  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: ruamel-yaml
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: runtime-dependencies
- dependency-name: scipy
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: runtime-dependencies
- dependency-name: sdtfile
  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 February 21, 2025 19:23
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Feb 21, 2025
@dependabot dependabot bot requested review from jsnel and s-weigand February 21, 2025 19:23
Copy link
Contributor

sourcery-ai bot commented Feb 21, 2025

Reviewer's Guide by Sourcery

This pull request bumps the runtime-dependencies group, updating multiple packages including asteval, netcdf4, numba, numpy, pandas, pydantic, ruamel-yaml, scipy, and sdtfile. These updates include bug fixes, performance improvements, security patches, and support for newer Python and NumPy versions. The numpy version constraint was also updated to allow versions up to, but not including, 2.3.

Updated class diagram for sdtfile

classDiagram
    class SdtFile {
        -file_header
        -setup_block
        -data_block
        -dll_data_block
        -fcs_data_block
        +__init__(filename)
        +close()
        +__str__()
    }
    note for SdtFile "Includes more information in str(SdtFile)"
    class FileRevision {
        -number
        -date
        -time
        -user
        -comment
        +subtype
    }
    note for FileRevision "Add subtype to FileRevision"
Loading

File-Level Changes

Change Details Files
Bumped asteval version to 1.0.6, including security-related fixes and improvements to error messages.
  • Dropped testing and support for Python3.8, added Python 3.13 support.
  • Implemented safe_getattr and safe_format functions.
  • Addressed bugs in UNSAFE_ATTRS and UNSAFE_ATTRS_DTYPES usage.
  • Made procedure attributes private to curb access to AST nodes.
  • Improved error messages using ast functions.
  • Removed import of numpy.linalg.
  • Updated documentation for security advisory.
pyproject.toml
Updated netcdf4 to version 1.7.2, introducing static type hints and exposing nc_rc_set and nc_rc_get functions.
  • Added static type hints.
  • Exposed nc_rc_set and nc_rc_get via rc_set, rc_get module functions.
  • Added Variable.get_fill_value and allowed fill_value='default' to set _FillValue attribute using default fill values.
  • Fixed NETCDF3 endian error.
  • Supported os.PathLike arguments for Dataset.fromcdl.
  • Raised 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
Upgraded numba to version 0.61.0, adding Python 3.13 and NumPy 2.1 support.
  • Added Python 3.13 support.
  • Added NumPy 2.1 support.
pyproject.toml
Advanced numpy to version 2.2.3, which includes typing improvements and fixes for free threaded Python.
  • Fixed data race in np.repeat.
  • Fixed from_float_positional errors for huge pads.
  • Updated highway to the latest version.
  • Added cpp atomic support.
  • Fixed timedelta64.divmod and timedelta64.mod typing.
  • Fixed missing typing information of set_printoptions.
  • Fixed incorrect bytes to stringdtype coercion.
  • Stubbed numpy.matlib and numpy.testing modules.
pyproject.toml
Incremented pandas version to 2.2.3, incorporating bug fixes and performance improvements.
  • Relaxed cython bound.
  • Built wheels for Python 3.13 on aarch64.
  • Fixed bad Cython annotation.
  • Removed ops div class to solve a specific issue.
  • Debugged failing ARM builds.
pyproject.toml
Advanced pydantic to version 2.10.6, which includes fixes for JSON Schema reference collection and URL python serialization.
  • Fixed JSON Schema reference collection with 'examples' keys.
  • Fixed URL python serialization.
  • Removed custom MRO implementation of Pydantic models.
  • Bumped pydantic-core to v2.27.2.
  • Fixed comparison of AnyUrl objects.
  • Properly fetched PEP 695 type params for functions.
  • Included JSON Schema input core schema in function schemas.
  • Added len to _BaseUrl to avoid TypeError.
  • Ensured the type reference is removed from the seen references.
  • Set fields when defer_build is set on Pydantic dataclasses.
  • Do not resolve the JSON Schema reference for dict core schema keys.
  • Used the globals of the function when evaluating the return type for PlainSerializer and WrapSerializer functions.
pyproject.toml
Updated ruamel-yaml to version 0.18.10. pyproject.toml
Advanced scipy to version 1.15.2, a bug-fix release with free-threaded Python 3.13 wheels for Linux ARM platform.
  • Wrapped median_filter stability.
  • Bumped test tolerance for integrate.cumulative_simpson.
  • Addressed pearsonr SIMD-related shim.
pyproject.toml
Advanced sdtfile to version 2024.12.6, including fixes for reading MeasureInfo fields and parsing SetupBlock binary structures.
  • Fixed read 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

Tips and commands

Interacting with Sourcery

  • Trigger a new review: Comment @sourcery-ai review on the pull request.
  • Continue discussions: Reply directly to Sourcery's review comments.
  • Generate a GitHub issue from a review comment: Ask Sourcery to create an
    issue from a review comment by replying to it. You can also reply to a
    review comment with @sourcery-ai issue to create an issue from it.
  • Generate a pull request title: Write @sourcery-ai anywhere in the pull
    request title to generate a title at any time. You can also comment
    @sourcery-ai title on the pull request to (re-)generate the title at any time.
  • Generate a pull request summary: Write @sourcery-ai summary anywhere in
    the pull request body to generate a PR summary at any time exactly where you
    want it. You can also comment @sourcery-ai summary on the pull request to
    (re-)generate the summary at any time.
  • Generate reviewer's guide: Comment @sourcery-ai guide on the pull
    request to (re-)generate the reviewer's guide at any time.
  • Resolve all Sourcery comments: Comment @sourcery-ai resolve on the
    pull request to resolve all Sourcery comments. Useful if you've already
    addressed all the comments and don't want to see them anymore.
  • Dismiss all Sourcery reviews: Comment @sourcery-ai dismiss on the pull
    request to dismiss all existing Sourcery reviews. Especially useful if you
    want to start fresh with a new review - don't forget to comment
    @sourcery-ai review to trigger a new review!
  • Generate a plan of action for an issue: Comment @sourcery-ai plan on
    an issue to generate a plan of action for it.

Customizing Your Experience

Access your dashboard to:

  • Enable or disable review features such as the Sourcery-generated pull request
    summary, the reviewer's guide, and others.
  • Change the review language.
  • Add, remove or edit custom review instructions.
  • Adjust other review settings.

Getting Help

Copy link
Contributor

@sourcery-ai sourcery-ai bot left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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!

Copy link
Contributor

Binder 👈 Launch a binder notebook on branch glotaran/pyglotaran/dependabot/pip/staging/runtime-dependencies-c3ca243d44

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
dependencies Pull requests that update a dependency file python Pull requests that update Python code
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants