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Chore(deps): Bump the python-packages group with 8 updates #321

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Updates the requirements on numpy, torch, torchvision, tifffile, pydantic, typer, scikit-image and protobuf to permit the latest version.
Updates numpy 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 torch to 2.5.1

Release notes

Sourced from torch's releases.

PyTorch 2.5.1: bug fix release

This release is meant to fix the following regressions:

Besides the regression fixes, the release includes several documentation updates.

See release tracker pytorch/pytorch#132400 for additional information.

Changelog

Sourced from torch's changelog.

Releasing PyTorch

Release Compatibility Matrix

Following is the Release Compatibility Matrix for PyTorch releases:

... (truncated)

Commits

Updates torchvision to 0.20.1

Commits

Updates tifffile to 2024.9.20

Release notes

Sourced from tifffile's releases.

v2024.9.20

Read and write TIFF files

Tifffile is a Python library to

  1. store NumPy arrays in TIFF (Tagged Image File Format) files, and
  2. read image and metadata from TIFF-like files used in bioimaging.

Image and metadata can be read from TIFF, BigTIFF, OME-TIFF, GeoTIFF, Adobe DNG, ZIF (Zoomable Image File Format), MetaMorph STK, Zeiss LSM, ImageJ hyperstack, Micro-Manager MMStack and NDTiff, SGI, NIHImage, Olympus FluoView and SIS, ScanImage, Molecular Dynamics GEL, Aperio SVS, Leica SCN, Roche BIF, PerkinElmer QPTIFF (QPI, PKI), Hamamatsu NDPI, Argos AVS, and Philips DP formatted files.

Image data can be read as NumPy arrays or Zarr arrays/groups from strips, tiles, pages (IFDs), SubIFDs, higher order series, and pyramidal levels.

Image data can be written to TIFF, BigTIFF, OME-TIFF, and ImageJ hyperstack compatible files in multi-page, volumetric, pyramidal, memory-mappable, tiled, predicted, or compressed form.

Many compression and predictor schemes are supported via the imagecodecs library, including LZW, PackBits, Deflate, PIXTIFF, LZMA, LERC, Zstd, JPEG (8 and 12-bit, lossless), JPEG 2000, JPEG XR, JPEG XL, WebP, PNG, EER, Jetraw, 24-bit floating-point, and horizontal differencing.

Tifffile can also be used to inspect TIFF structures, read image data from multi-dimensional file sequences, write fsspec ReferenceFileSystem for TIFF files and image file sequences, patch TIFF tag values, and parse many proprietary metadata formats.

Changes

  • Fix writing colormap to ImageJ files (breaking).
  • Improve typing.
  • Remove support for Python 3.9.
Changelog

Sourced from tifffile's changelog.

2024.9.20

  • Pass 5107 tests.
  • Fix writing colormap to ImageJ files (breaking).
  • Improve typing.
  • Remove support for Python 3.9.

2024.8.30

  • Support writing OME Dataset and some StructuredAnnotations elements.

2024.8.28

  • Fix LSM scan types and dimension orders (#269, breaking).
  • Use IO[bytes] instead of BinaryIO for typing (#268).

2024.8.24

  • Do not remove trailing length-1 dimension writing non-shaped file (breaking).
  • Fix writing OME-TIFF with certain modulo axes orders.
  • Make imshow NaN aware.

2024.8.10

  • Relax bitspersample check for JPEG, JPEG2K, and JPEGXL compression (#265).

2024.7.24

  • Fix reading contiguous multi-page series via Zarr store (#67).

2024.7.21

  • Fix integer overflow in product function caused by numpy types.
  • Allow tag reader functions to fail.

2024.7.2

  • Enable memmap to create empty files with non-native byte order.
  • Deprecate Python 3.9, support Python 3.13.

2024.6.18

  • Ensure TiffPage.nodata is castable to dtype (breaking, #260).
  • Support Argos AVS slides.

2024.5.22

  • Derive TiffPages, TiffPageSeries, FileSequence, StoredShape from Sequence.
  • Truncate circular IFD chain, do not raise TiffFileError (breaking).
  • Deprecate access to TiffPages.pages and FileSequence.files.

... (truncated)

Commits

Updates pydantic to 2.10.3

Release notes

Sourced from pydantic's releases.

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

Changelog

Sourced from pydantic's changelog.

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

v2.10.2 (2024-11-25)

GitHub release

What's Changed

Fixes

v2.10.1 (2024-11-21)

GitHub release

What's Changed

Packaging

Fixes

... (truncated)

Commits
  • c326748 Prep for v2.10.3 release (#11038)
  • 68d35bf Fix url json schema in serialization mode (#11035)
  • fa69b4c Add a default_factory_takes_validated_data property to FieldInfo (#11034)
  • 435a703 Fix host required enforcement for urls to be compatible with v2.9 behavior (#...
  • b2c4548 Use the globals of the function when evaluating the return type for `PlainSer...
  • cb962c1 Do not resolve the JSON Schema reference for dict core schema keys (#10989)
  • 10ebcdf Set fields when defer_build is set on Pydantic dataclasses (#10984)
  • fe32515 Prepare for v2.10.2 release (#10982)
  • 226cfaf Hide BaseModel.__replace__ definition from type checkers (#10979)
  • 02229a6 hashing support for urls (#10975)
  • Additional commits viewable in compare view

Updates typer from 0.12.3 to 0.15.1

Release notes

Sourced from typer's releases.

0.15.1

Features

  • 🗑️ Deprecate shell_complete and continue to use autocompletion for CLI parameters. PR #974 by @​svlandeg.

Docs

Internal

0.15.0

Features

Internal

0.14.0

Breaking Changes

  • 🔥 Remove auto naming of groups added via add_typer based on the group's callback function name. PR #1052 by @​patrick91.

Before, it was supported to infer the name of a command group from the callback function name in the sub-app, so, in this code:

import typer
app = typer.Typer()
users_app = typer.Typer()
app.add_typer(users_app)
@​users_app.callback()
def users():  # <-- This was the inferred command group name
"""
Manage users in the app.
</tr></table>

... (truncated)

Changelog

Sourced from typer's changelog.

0.15.1

Features

  • 🗑️ Deprecate shell_complete and continue to use autocompletion for CLI parameters. PR #974 by @​svlandeg.

Docs

Internal

0.15.0

Features

Internal

0.14.0

Breaking Changes

  • 🔥 Remove auto naming of groups added via add_typer based on the group's callback function name. PR #1052 by @​patrick91.

Before, it was supported to infer the name of a command group from the callback function name in the sub-app, so, in this code:

import typer
app = typer.Typer()
users_app = typer.Typer()
app.add_typer(users_app)
@​users_app.callback()
</tr></table>

... (truncated)

Commits
  • 0b89650 🔖 Release version 0.15.1
  • bd89bf6 📝 Update release notes
  • 3b9ce47 ✏️ Fix a few typos in the source and documentation (#1028)
  • 95ba85f 📝 Update release notes
  • dbc335b 📝 Fix minor inconsistencies and typos in tutorial (#1067)
  • b88c327 📝 Update release notes
  • d8e56e2 🗑️ Deprecate shell_complete and continue to use autocompletion for CLI pa...
  • 5f378ee 📝 Update release notes
  • b826dc4 ✏️ Fix a few small typos in the documentation (#1077)
  • 9be60da 📝 Update release notes
  • Additional commits viewable in compare view

Updates scikit-image to 0.24.0

Release notes

Sourced from scikit-image's releases.

v0.24.0

scikit-image 0.24.0

We're happy to announce the release of scikit-image 0.24.0!

Highlights

  • Add new class skimage.transform.ThinPlateSplineTransform, which can estimate and model non-linear transforms with thin-plate splines and allows image warping with skimage.transform.warp (#7040).

New Features

  • Add new class skimage.transform.ThinPlateSplineTransform, which can estimate and model non-linear transforms with thin-plate splines and allows image warping with skimage.transform.warp (#7040).
  • Add skimage.morphology.remove_objects_by_distance, which removes labeled objects, ordered by size (default), until the remaining objects are a given distance apart (#4165).

Performance

  • In skimage.feature.corner_fast, test four directions earlier, which should more than half the computation time for most cases (#7394).

Documentation

  • Remove obsolete instruction about documenting changes (#7321).
  • Clarify description of data_range parameter in skimage.metrics.structural_similarity (#7345).
  • Update release process notes (#7402).
  • Fix typo in docstring of skimage.measure.regionprops (#7405).
  • Fix typos in skimage.measure.find_contours (#7411).
  • Add algorithmic complexity description + suggested alternatives to skimage.restoration.rolling_ball docstring (#7424).
  • Remove ineffective PR contribution clause (#7429).
  • Clarify objection period for lazy consensus in SKIP 1 (#7020).
  • Add a new gallery example "Use thin-plate splines for image warping" (#7040).
  • Add a new gallery example on "Removing objects" based on their size or distance (#4165).

Infrastructure

  • Escape user-controlled variables in GA workflow (#7415).
  • Add generation of GitHub artifact attestations to built sdist and wheels before upload to PyPI (#7427).
  • For publishing actions use the full length commit SHA (#7433).
  • Be mindful of resources by canceling in-progress workflows (#7436).
  • Add out-of-tree Pyodide builds in CI for scikit-image (#7350).

Maintenance

  • Replace deprecated nose style setup/teardown with autouse fixtures (#7343).
  • Temporarily pin macos-12 runner in CI (#7408).
  • Fix NumPy2 dtype promotion issues in pywt dependent code (#7414).
  • In skimage.util.compare_images, deprecate the parameter image2. Instead use image0, image1 to pass the compared images. Furthermore, all other parameters will be turned into keyword-only parameters once the deprecation is complete (#7322).
  • Add support back for Python 3.9 to enhance compatibility with Numpy 2 (#7412).
  • Disable ruff/pyupgrade rule UP038 (#7430).
  • Stop verifying wheel attestations temporarily (#7444).

Contributors

... (truncated)

Changelog

Sourced from scikit-image's changelog.

  • 0.24.0rc0.dev0 # development version for 0.24.0 first release candidate

Process

  • To debug building and testing wheels via CI, push to a branch named maintenance/anything.

    Once everything works as intended, remove those branches and proceed.

  • Set release variables:

    export VERSION=<version number>
export PREVIOUS=<previous version number>
export ORG="scikit-image"
export REPO="scikit-image"

    If this is a prerelease:

    export NOTES="doc/source/release_notes/release_dev.rst"

    If this is release:

    export NOTES="doc/source/release_notes/release_${VERSION}.rst"
git rm doc/source/release_notes/release_dev.rst

  • Autogenerate release notes:

    changelist ${ORG}/${REPO} v${PREVIOUS} main --version ${VERSION}  --out ${NOTES} --format rst
changelist ${ORG}/${REPO} v${PREVIOUS} main --version ${VERSION}  --out ${VERSION}.md

  • If you want, you can review the release notes:

    • Scan the PR titles for highlights and mention these in the relevant sections of the notes. Ideally, all changed API objects are mentioned by name, e.g. a new parameter or a deprecated function.

    • Check for duplicate names in the automatically generated list of contributors and reviewers.

    • Append the release date to the title similar to previous iterations.

  • If this is a release:

    • (Only needed if you create a new branch) update the file skimage/data/_fetchers.py to point the pooch repository to the new branch instead of main during testing. Look for the parameter version_dev="main", for pooch.create and change it to the newly created branch name.

... (truncated)

Commits

Updates protobuf from 3.20.3 to 5.29.1

Commits
  • 796e49f Updating version.json and repo version numbers to: 29.1
  • ba6da44 Rename maven to protobuf_maven in MODULE.bazel (#18641) (#19477)
  • 5864b50 Revert "Remove deprecated service.py usages from test". For 29.x only (#19434)
  • e0a3978 Merge pull request #19425 from protocolbuffers/29.x-202411271837
  • 9e78ac7 Updating version.json and repo version numbers to: 29.1-dev
  • 2d4414f Updating version.json and repo version numbers to: 29.0
  • 870e599 Revert upgrade to rules_java 8.3.1. This is a partial roll-back of fb8ee79 (#...
  • 02cffa4 Fix typo in BCR maintainer name config for acozzette@ (#19307)
  • 7537b03 Remove Bazel 6 in BCR presubmits (#19309)
  • 325aa80 Merge pull request #19305 from protocolbuffers/29.x-202411182222
  • Additional commits viewable in compare view

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@dependabot
Chore(deps): Bump the python-packages group with 8 updates
25092d4 
Updates the requirements on [numpy](https://github.com/numpy/numpy), [torch](https://github.com/pytorch/pytorch), [torchvision](https://github.com/pytorch/vision), [tifffile](https://github.com/cgohlke/tifffile), [pydantic](https://github.com/pydantic/pydantic), [typer](https://github.com/fastapi/typer), [scikit-image](https://github.com/scikit-image/scikit-image) and [protobuf](https://github.com/protocolbuffers/protobuf) to permit the latest version.

Updates `numpy` 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@v0.2.0...v2.2.0)

Updates `torch` to 2.5.1
- [Release notes](https://github.com/pytorch/pytorch/releases)
- [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md)
- [Commits](pytorch/pytorch@v2.0.0...v2.5.1)

Updates `torchvision` to 0.20.1
- [Release notes](https://github.com/pytorch/vision/releases)
- [Commits](pytorch/vision@v0.1.5...v0.20.1)

Updates `tifffile` to 2024.9.20
- [Release notes](https://github.com/cgohlke/tifffile/releases)
- [Changelog](https://github.com/cgohlke/tifffile/blob/master/CHANGES.rst)
- [Commits](cgohlke/tifffile@v2018.10.18...v2024.9.20)

Updates `pydantic` to 2.10.3
- [Release notes](https://github.com/pydantic/pydantic/releases)
- [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md)
- [Commits](pydantic/pydantic@v2.5.0...v2.10.3)

Updates `typer` from 0.12.3 to 0.15.1
- [Release notes](https://github.com/fastapi/typer/releases)
- [Changelog](https://github.com/fastapi/typer/blob/master/docs/release-notes.md)
- [Commits](fastapi/typer@0.12.3...0.15.1)

Updates `scikit-image` to 0.24.0
- [Release notes](https://github.com/scikit-image/scikit-image/releases)
- [Changelog](https://github.com/scikit-image/scikit-image/blob/main/RELEASE.txt)
- [Commits](scikit-image/scikit-image@v0.1...v0.24.0)

Updates `protobuf` from 3.20.3 to 5.29.1
- [Release notes](https://github.com/protocolbuffers/protobuf/releases)
- [Changelog](https://github.com/protocolbuffers/protobuf/blob/main/protobuf_release.bzl)
- [Commits](protocolbuffers/protobuf@v3.20.3...v5.29.1)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
  dependency-group: python-packages
- dependency-name: torch
  dependency-type: direct:production
  dependency-group: python-packages
- dependency-name: torchvision
  dependency-type: direct:production
  dependency-group: python-packages
- dependency-name: tifffile
  dependency-type: direct:production
  dependency-group: python-packages
- dependency-name: pydantic
  dependency-type: direct:production
  dependency-group: python-packages
- dependency-name: typer
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: scikit-image
  dependency-type: direct:production
  dependency-group: python-packages
- dependency-name: protobuf
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: python-packages
...

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@dependabot dependabot bot added the dependencies Pull requests that update a dependency file label Dec 9, 2024
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