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.

Sign up for GitHub

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

Jump to bottom

Bump the runtime-dependencies group across 1 directory with 8 updates #1567

Merged
merged 4 commits into from
Dec 29, 2024
Merged

Bump the runtime-dependencies group across 1 directory with 8 updates #1567

merged 4 commits into from
Dec 29, 2024

Conversation

dependabot[bot]
Copy link
Contributor

@dependabot dependabot bot commented on behalf of github Dec 29, 2024 •
edited by sourcery-ai bot
Loading

Bumps the runtime-dependencies group with 8 updates in the / directory:

Package From To
asteval 1.0.3 1.0.5
attrs 24.2.0 24.3.0
click 8.1.7 8.1.8
netcdf4 1.7.1.post2 1.7.2
numpy 2.0.2 2.2.1
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 attrs from 24.2.0 to 24.3.0

Commits

Updates click from 8.1.7 to 8.1.8

Release notes

Sourced from click's releases.

8.1.8

This is the Click 8.1.8 fix release, which fixes bugs but does not otherwise change behavior and should not result in breaking changes compared to the latest feature release.

PyPI: https://pypi.org/project/click/8.1.8/ Changes: https://click.palletsprojects.com/en/stable/changes/#version-8-1-8 Milestone https://github.com/pallets/click/milestones/23?closed=1

  • Fix an issue with type hints for click.open_file(). #2717
  • Fix issue where error message for invalid click.Path displays on multiple lines. #2697
  • Fixed issue that prevented a default value of "" from being displayed in the help for an option. #2500
  • The test runner handles stripping color consistently on Windows. #2705
  • Show correct value for flag default when using default_map. #2632
  • Fix click.echo(color=...) passing color to coloroma so it can be forced on Windows. #2606.
  • More robust bash version check, fixing problem on Windows with git-bash. #2638
  • Cache the help option generated by the help_option_names setting to respect its eagerness. #2811
  • Replace uses of os.system with subprocess.Popen. #1476
  • Exceptions generated during a command will use the context's color setting when being displayed. #2193
  • Error message when defining option with invalid name is more descriptive. #2452
  • Refactor code generating default --help option to deduplicate code. #2563
  • Test CLIRunner resets patched _compat.should_strip_ansi. #2732
Changelog

Sourced from click's changelog.

Version 8.1.8

Unreleased

  • Fix an issue with type hints for click.open_file(). :issue:2717
  • Fix issue where error message for invalid click.Path displays on multiple lines. :issue:2697
  • Fixed issue that prevented a default value of "" from being displayed in the help for an option. :issue:2500
  • The test runner handles stripping color consistently on Windows. :issue:2705
  • Show correct value for flag default when using default_map. :issue:2632
  • Fix click.echo(color=...) passing color to coloroma so it can be forced on Windows. :issue:2606.
Commits

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 2.2.1

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

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]

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

Build:

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

@dependabot
Bump the runtime-dependencies group across 1 directory with 8 updates
95e098b 
Bumps the runtime-dependencies group with 8 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| [asteval](https://github.com/lmfit/asteval) | `1.0.3` | `1.0.5` |
| [attrs](https://github.com/sponsors/hynek) | `24.2.0` | `24.3.0` |
| [click](https://github.com/pallets/click) | `8.1.7` | `8.1.8` |
| [netcdf4](https://github.com/Unidata/netcdf4-python) | `1.7.1.post2` | `1.7.2` |
| [numpy](https://github.com/numpy/numpy) | `2.0.2` | `2.2.1` |
| [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 `attrs` from 24.2.0 to 24.3.0
- [Commits](https://github.com/sponsors/hynek/commits)

Updates `click` from 8.1.7 to 8.1.8
- [Release notes](https://github.com/pallets/click/releases)
- [Changelog](https://github.com/pallets/click/blob/main/CHANGES.rst)
- [Commits](pallets/click@8.1.7...8.1.8)

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 2.2.1
- [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...v2.2.1)

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: attrs
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: runtime-dependencies
- dependency-name: click
  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 29, 2024 18:54
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Dec 29, 2024
@dependabot dependabot bot requested review from jsnel and s-weigand December 29, 2024 18:54
@sourcery-ai Sourcery AI
Copy link
Contributor

sourcery-ai bot commented Dec 29, 2024 •
edited
Loading

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 1.0.3 to 1.0.5
  • Improved error management and exception handling
  • Added more tests for exception handling
 /setup.cfg
/requirements_dev.txt
Update attrs from 24.2.0 to 24.3.0 /setup.cfg
/requirements_dev.txt
Update click from 8.1.7 to 8.1.8
  • Fixed type hints for click.open_file()
  • Fixed issue where error message for invalid click.Path displayed on multiple lines
  • Fixed issue that prevented default value of "" from being displayed in help
  • Test runner handles stripping color consistently on Windows
  • Improved bash version check
 /setup.cfg
/requirements_dev.txt
Update netcdf4 from 1.7.1.post2 to 1.7.2
  • Added static type hints
  • Exposed nc_rc_set, nc_rc_get functions
  • Added Variable.get_fill_value and support for fill_value='default'
  • Fixed NETCDF3 endian error
 /setup.cfg
/requirements_dev.txt
Update numpy from 2.0.2 to 2.2.1
  • Fixed use-after-free error in npy_hashtable.cpp
  • Fixed falsely rejected value types in ndarray.setitem
  • Fixed segfault in stringdtype lexsort
  • Allowed None in operand sequence of nditer
 /setup.cfg
/requirements_dev.txt
Update pandas from 2.2.2 to 2.2.3
  • Built wheels for Python 3.13 on aarch64
  • Fixed bad Cython annotation
  • Removed ops div class to solve #2137
 /setup.cfg
/requirements_dev.txt
Update sdtfile from 2024.5.24 to 2024.12.6
  • 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
 /setup.cfg
/requirements_dev.txt
Update xarray from 2024.9.0 to 2024.11.0
  • Fixed inadvertent deep-copying of child data in DataTree
  • Raise ValueError for unmatching chunks length in DataArray.chunk()
  • Added DataTree.persist
  • Used same function to floatize coords in polyfit and polyval
  • Fixed writing of DataTree subgroups to zarr or netCDF
 /setup.cfg
/requirements_dev.txt
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.
  • Generate a pull request title: Write @sourcery-ai anywhere in the pull
    request title to generate a 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. You can also use
    this command to specify where the summary should be inserted.

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

sourcery-ai[bot]
sourcery-ai bot reviewed Dec 29, 2024
View reviewed changes
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!

@s-weigand s-weigand force-pushed the dependabot/pip/runtime-dependencies-71c0a2adaa branch from 0e1b608 to 31b2151 Compare December 29, 2024 22:17
@sonarqubecloud SonarQubeCloud
Copy link

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

s-weigand
s-weigand approved these changes Dec 29, 2024
View reviewed changes
Copy link
Member

@s-weigand s-weigand left a comment

Choose a reason for hiding this comment

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

I downgraded numpy again because there currently isn't a numba version that officially supports it.
I also fixed the old breaking definition of intersphinx_mapping that was breaking the docs and fixed 2 more deprecation warnings from sphinx.

@s-weigand s-weigand merged commit 084956a into main Dec 29, 2024
37 checks passed
@s-weigand s-weigand deleted the dependabot/pip/runtime-dependencies-71c0a2adaa branch December 29, 2024 22:26
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@sourcery-ai sourcery-ai[bot] sourcery-ai[bot] left review comments

@s-weigand s-weigand s-weigand approved these changes

@jsnel jsnel Awaiting requested review from jsnel

Assignees

@jsnel jsnel

@s-weigand s-weigand

Labels
dependencies Pull requests that update a dependency file python Pull requests that update Python code
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@s-weigand @jsnel