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Bump the pip-all-updates group with 7 updates #295

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merged 1 commit into from
Jan 7, 2025
Merged

Bump the pip-all-updates group with 7 updates #295

merged 1 commit into from
Jan 7, 2025

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@dependabot dependabot bot commented on behalf of github Jan 1, 2025

Bumps the pip-all-updates group with 7 updates:

Package From To
coverage 7.6.8 7.6.10
matplotlib 3.9.3 3.10.0
pytest 8.3.3 8.3.4
ruff 0.8.1 0.8.4
scikit-image 0.24.0 0.25.0
scikit-learn 1.5.2 1.6.0
transformers 4.46.3 4.47.1

Updates coverage from 7.6.8 to 7.6.10

Changelog

Sourced from coverage's changelog.

Version 7.6.10 — 2024-12-26

  • Fix: some descriptions of missing branches in HTML and LCOV reports were incorrect when multi-line statements were involved (issue 1874_ and issue 1875_). These are now fixed.

  • Fix: Python 3.14 defers evaluation of annotations <pep649_>_ by moving them into separate code objects. That code is rarely executed, so coverage.py would mark them as missing, as reported in issue 1908_. Now they are ignored by coverage automatically.

  • Fixed an obscure and mysterious problem on PyPy 3.10 seemingly involving mocks, imports, and trace functions: issue 1902_. To be honest, I don't understand the problem or the solution, but git bisect helped find it, and now it's fixed.

  • Docs: re-wrote the :ref:subprocess page to put multiprocessing first and to highlight the correct use of :class:multiprocessing.Pool <python:multiprocessing.pool.Pool>.

.. _issue 1874: nedbat/coveragepy#1874 .. _issue 1875: nedbat/coveragepy#1875 .. _issue 1902: nedbat/coveragepy#1902 .. _issue 1908: nedbat/coveragepy#1908 .. _pep649: https://docs.python.org/3.14/whatsnew/3.14.html#pep-649-deferred-evaluation-of-annotations

.. _changes_7-6-9:

Version 7.6.9 — 2024-12-06

  • Fix: Tomas Uribe fixed <pull 1901_>_ a performance problem in the XML report. Large code bases should produce XML reports much faster now.

.. _pull 1901: nedbat/coveragepy#1901

.. _changes_7-6-8:

Commits
  • f0dcf65 docs: sample HTML for 7.6.10
  • 0f26f35 docs: prep for 7.6.10
  • 81c5e43 docs: rewrite the subprocess page
  • 878410c chore: make doc_upgrade
  • f1d320d chore: make upgrade
  • 67f1440 debug: this condition is never true. really?
  • c85eaba fix: multi-line statements no longer confuse branch target descriptions. #187...
  • 73e58fa refactor: clarify the code that fixes with-statement exits
  • e16c9cc typo: backslask
  • 865fd7f chore: bump the action-dependencies group with 4 updates (#1909)
  • Additional commits viewable in compare view

Updates matplotlib from 3.9.3 to 3.10.0

Release notes

Sourced from matplotlib's releases.

REL: v3.10.0

Highlights of this release include:

- Preliminary support for free-threaded CPython 3.13
- New more-accessible color cycle
- Dark-mode diverging colormaps
- Exception handling control
- InsetIndicator artist
- FillBetweenPolyCollection
- Fill between 3D lines
- Data in 3D plots can now be dynamically clipped to the axes view limits
- Rotating 3d plots with the mouse
- Increased Figure limits with Agg renderer
- Subfigures no longer provisional
- Subfigures are now added in row-major order

Matplotlib v3.10.0rc1

This is the first release candidate for Matplotlib 3.10.0

REL: 3.9.4

This is the fourth bugfix release of the 3.9.x series.

This release contains two bug-fixes:

  • Fix toolbar icons in GTK backend
  • Fix Poly3DCollection initialization with list of lists
Commits
  • 8d64f03 REL: v3.10.0 release
  • d9dfee8 [doc] Fix dead links
  • 87a603f Update release notes for 3.10.0
  • cdecf97 Update github stats for 3.10
  • b8d19bd Merge pull request #29306 from meeseeksmachine/auto-backport-of-pr-29242-on-v...
  • a42d0ed Backport PR #29242: DOC: Add kwdoc list to scatter() docstring
  • 1900640 Merge pull request #29299 from QuLogic/merge-v39x
  • 815389c Merge branch 'v3.9.x' into v3.10.x
  • 73873c0 DOC: Create release notes for 3.9.4
  • 9d17a2b DOC: Add Zenodo DOI for 3.9.4
  • Additional commits viewable in compare view

Updates pytest from 8.3.3 to 8.3.4

Release notes

Sourced from pytest's releases.

8.3.4

pytest 8.3.4 (2024-12-01)

Bug fixes

  • #12592: Fixed KeyError{.interpreted-text role="class"} crash when using --import-mode=importlib in a directory layout where a directory contains a child directory with the same name.

  • #12818: Assertion rewriting now preserves the source ranges of the original instructions, making it play well with tools that deal with the AST, like executing.

  • #12849: ANSI escape codes for colored output now handled correctly in pytest.fail{.interpreted-text role="func"} with [pytrace=False]{.title-ref}.

  • #9353: pytest.approx{.interpreted-text role="func"} now uses strict equality when given booleans.

Improved documentation

  • #10558: Fix ambiguous docstring of pytest.Config.getoption{.interpreted-text role="func"}.

  • #10829: Improve documentation on the current handling of the --basetemp option and its lack of retention functionality (temporary directory location and retention{.interpreted-text role="ref"}).

  • #12866: Improved cross-references concerning the recwarn{.interpreted-text role="fixture"} fixture.

  • #12966: Clarify filterwarnings{.interpreted-text role="ref"} docs on filter precedence/order when using multiple @pytest.mark.filterwarnings <pytest.mark.filterwarnings ref>{.interpreted-text role="ref"} marks.

Contributor-facing changes

  • #12497: Fixed two failing pdb-related tests on Python 3.13.
Commits
  • 53f8b4e Update pypa/gh-action-pypi-publish to v1.12.2
  • 98dff36 Prepare release version 8.3.4
  • 1b474e2 approx: use exact comparison for bool (#13013)
  • b541721 docs: Fix wrong statement about sys.modules with importlib import mode (#1298...
  • 16cb87b pytest.fail: fix ANSI escape codes for colored output (#12959) (#12990)
  • be6bc81 Issue #12966 Clarify filterwarnings docs on precedence when using multiple ma...
  • 7aeb72b Improve docs on basetemp and retention (#12912) (#12928)
  • c875841 Merge pull request #12917 from pytest-dev/patchback/backports/8.3.x/ded1f44e5...
  • 6502816 Merge pull request #12913 from jakkdl/dontfailonbadpath
  • 52135b0 Merge pull request #12885 from The-Compiler/pdb-py311 (#12887)
  • Additional commits viewable in compare view

Updates ruff from 0.8.1 to 0.8.4

Release notes

Sourced from ruff's releases.

0.8.4

Release Notes

Preview features

  • [airflow] Extend AIR302 with additional functions and classes (#15015)
  • [airflow] Implement moved-to-provider-in-3 for modules that has been moved to Airflow providers (AIR303) (#14764)
  • [flake8-use-pathlib] Extend check for invalid path suffix to include the case "." (PTH210) (#14902)
  • [perflint] Fix panic in PERF401 when list variable is after the for loop (#14971)
  • [perflint] Simplify finding the loop target in PERF401 (#15025)
  • [pylint] Preserve original value format (PLR6104) (#14978)
  • [ruff] Avoid false positives for RUF027 for typing context bindings (#15037)
  • [ruff] Check for ambiguous pattern passed to pytest.raises() (RUF043) (#14966)

Rule changes

  • [flake8-bandit] Check S105 for annotated assignment (#15059)
  • [flake8-pyi] More autofixes for redundant-none-literal (PYI061) (#14872)
  • [pydocstyle] Skip leading whitespace for D403 (#14963)
  • [ruff] Skip SQLModel base classes for mutable-class-default (RUF012) (#14949)

Bug

  • [perflint] Parenthesize walrus expressions in autofix for manual-list-comprehension (PERF401) (#15050)

Server

  • Check diagnostic refresh support from client capability which enables dynamic configuration for various editors (#15014)

Contributors

... (truncated)

Changelog

Sourced from ruff's changelog.

0.8.4

Preview features

  • [airflow] Extend AIR302 with additional functions and classes (#15015)
  • [airflow] Implement moved-to-provider-in-3 for modules that has been moved to Airflow providers (AIR303) (#14764)
  • [flake8-use-pathlib] Extend check for invalid path suffix to include the case "." (PTH210) (#14902)
  • [perflint] Fix panic in PERF401 when list variable is after the for loop (#14971)
  • [perflint] Simplify finding the loop target in PERF401 (#15025)
  • [pylint] Preserve original value format (PLR6104) (#14978)
  • [ruff] Avoid false positives for RUF027 for typing context bindings (#15037)
  • [ruff] Check for ambiguous pattern passed to pytest.raises() (RUF043) (#14966)

Rule changes

  • [flake8-bandit] Check S105 for annotated assignment (#15059)
  • [flake8-pyi] More autofixes for redundant-none-literal (PYI061) (#14872)
  • [pydocstyle] Skip leading whitespace for D403 (#14963)
  • [ruff] Skip SQLModel base classes for mutable-class-default (RUF012) (#14949)

Bug

  • [perflint] Parenthesize walrus expressions in autofix for manual-list-comprehension (PERF401) (#15050)

Server

  • Check diagnostic refresh support from client capability which enables dynamic configuration for various editors (#15014)

0.8.3

Preview features

  • Fix fstring formatting removing overlong implicit concatenated string in expression part (#14811)
  • [airflow] Add fix to remove deprecated keyword arguments (AIR302) (#14887)
  • [airflow]: Extend rule to include deprecated names for Airflow 3.0 (AIR302) (#14765 and #14804)
  • [flake8-bugbear] Improve error messages for except* (B025, B029, B030, B904) (#14815)
  • [flake8-bugbear] itertools.batched() without explicit strict (B911) (#14408)
  • [flake8-use-pathlib] Dotless suffix passed to Path.with_suffix() (PTH210) (#14779)
  • [pylint] Include parentheses and multiple comparators in check for boolean-chained-comparison (PLR1716) (#14781)
  • [ruff] Do not simplify round() calls (RUF046) (#14832)
  • [ruff] Don't emit used-dummy-variable on function parameters (RUF052) (#14818)
  • [ruff] Implement if-key-in-dict-del (RUF051) (#14553)
  • [ruff] Mark autofix for RUF052 as always unsafe (#14824)
  • [ruff] Teach autofix for used-dummy-variable about TypeVars etc. (RUF052) (#14819)

Rule changes

  • [flake8-bugbear] Offer unsafe autofix for no-explicit-stacklevel (B028) (#14829)
  • [flake8-pyi] Skip all type definitions in string-or-bytes-too-long (PYI053) (#14797)
  • [pyupgrade] Do not report when a UTF-8 comment is followed by a non-UTF-8 one (UP009) (#14728)

... (truncated)

Commits
  • 3bb0dac Bump version to 0.8.4 (#15064)
  • 40cba5d [red-knot] Cleanup various todo_type!() messages (#15063)
  • 596d80c [perflint] Parenthesize walrus expressions in autofix for `manual-list-comp...
  • d8b9a36 Disable actionlint hook by default when running pre-commit locally (#15061)
  • 85e71ba [flake8-bandit] Check S105 for annotated assignment (#15059)
  • 2802cbd Don't special-case class instances in unary expression inference (#15045)
  • ed2bce6 [red-knot] Report invalid exceptions (#15042)
  • f0012df Fix typos in RUF043.py (#15044)
  • 0fc4e8f Introduce InferContext (#14956)
  • ac81c72 [ruff] Ambiguous pattern passed to pytest.raises() (RUF043) (#14966)
  • Additional commits viewable in compare view

Updates scikit-image from 0.24.0 to 0.25.0

Release notes

Sourced from scikit-image's releases.

v0.25.0

scikit-image 0.25.0

We're happy to announce the release of scikit-image 0.25.0!

New Features

  • Add the new Gray-Level Co-occurrence Matrix (GLCM) properties "mean", "variance", "standard deviation" and "entropy" to skimage.feature.texture.graycoprops (#7375).
  • Add the new skimage.morphology.footprint_rectangle supporting generation of rectangular or hyper-rectangular footprints in one function (#7566).

API Changes

  • Complete the deprecation of and remove skimage.feature.plot_matches. Use skimage.feature.plot_matched_features going forward (#7487).
  • Deprecate skimage.io.imshow, skimage.io.imshow_collection and skimage.io.show. Please use matplotlib, napari, etc. to visualize images (#7508).
  • Remove deprecated skimage.morphology.skeletonize_3d; use skimage.morphology.skeletonize instead (#7572).
  • Deprecate skimage.io plugin infrastructure (#7353).
  • Switched to using the scipy.sparse array interface. For more details, see the note about the new scipy.sparse array interface here (#7576).
  • Deprecate skimage.morphology.rectangle in favor of the new function skimage.morphology.footprint_rectangle (#7566).
  • Deprecate skimage.morphology.square in favor of the new function skimage.morphology.footprint_rectangle (#7566).
  • Deprecate skimage.morphology.cube in favor of the new function skimage.morphology.footprint_rectangle (#7566).

Enhancements

  • Improve numerical stability of skimage.morphology.local_minima for extremely small floats (#7534).
  • Make sure that skimage.feature.plot_matched_features uses the same random colors, if matches_color isn't provided explicitly (#7541).
  • Allow passing a sequence of colors to the parameter matches_color in skimage.feature.plot_matched_features (#7541).

Performance

  • skimage.feature.peak_local_max will now skip unnecessary distance computations in the case of min_distance=1. This results in performance improvements to functions like skimage.feature.blob_dog, skimage.feature.blob_log, skimage.feature.blob_doh and skimage.feature.corner_peaks that call peak_local_max internally (#7548).
  • In skimage.featurepeak_local_max, skip unnecessary check for cases where min_distance > 1 is passed (#7548).

Bug Fixes

  • Ensure that skimage.morphology.remove_objects_by_distance doesn't fail if the given integer dtype cannot be safely cast to the architecture specific size of intp, e.g. on i386 architectures (#7453).
  • Fix degeneracy in skimage.draw.ellipsoid_stats when all semi-axes have the same length (#7473).
  • Prevent skimage.morphology.thin from accidentally modifying the input image in case it is of dtype uint8 (#7469).
  • Fix numerical precision error in skimage.measure.ransac. In some cases, ransac was stopping at the first iteration (#7065).
  • Fix numerical precision error in skimage.measure.ransac; very small probabilities lead to -0 number of max trials (#7496).
  • Ensure that RegionProperties objects returned by skimage.measure.regionprops can be deserialized with pickle (#7569).
  • Fix edge case where setting watershed_lines=True in skimage.segmentation.watershed resulted in an incorrect solution (#7071).
  • Fix the behavior of skimage.segmentation.watershed when the markers don't align with local minima by making sure every marker is evaluated before successive pixels (#7071).
  • Fix dtype promotion in skimage.segmentation.join_segmentations if numpy.uint is used with NumPy<2 (#7292).

Documentation

  • In skimage.morphology.skeletonize, clarify the expected image dtypes and how objects of different intensities are handled (#7456).
  • Fix example section in docstring of skimage.feature.graycomatrix (#7297).
  • Use conda-forge consistently in instructions for setting up the development environment (#7483).
  • Use new CITATION.cff instead of CITATION.bib (#7505).

... (truncated)

Changelog

Sourced from scikit-image's changelog.

How to make a new release of skimage

While following this guide, note down all the times that you need to consult a previous release manager, or that you find an instruction unclear. You will, of course, make a PR to update these notes after you are done with the release! ;-)

Before you start, make sure you have all the required write permissions (if not, you will need to ask an owner to grant you access), specifically to:

We use a variant of "semantic versioning", where version numbers are classified as v... By default, releases are made from the main branch as part of a linear release history and, as described below, are triggered by pushing a git tag to the scikit-image repository on github. If a patch release is required, a branch can be created from the appropriate point in main and the following instructions are still apt.

Example version number

  • 0.23.0rc0.dev0 # development version for 0.23.0 first release candidate
  • 0.23.0rc0 # 0.23.0 first release candidate
  • 0.23.0rc1.dev0 # development version for 0.23.0 second release candidate
  • 0.23.0 # 0.23.0 release
Commits

Updates scikit-learn from 1.5.2 to 1.6.0

Release notes

Sourced from scikit-learn's releases.

Scikit-learn 1.6.0

We're happy to announce the 1.6.0 release.

You can read the release highlights under https://scikit-learn.org/stable/auto_examples/release_highlights/plot_release_highlights_1_6_0.html and the long version of the change log under https://scikit-learn.org/stable/whats_new/v1.6.html

This version supports Python versions 3.9 to 3.13 and features an experimental support of free-threaded CPython.

You can upgrade with pip as usual:

pip install -U scikit-learn

The conda-forge builds can be installed using:

conda install -c conda-forge scikit-learn
Commits

Updates transformers from 4.46.3 to 4.47.1

Release notes

Sourced from transformers's releases.

v4.47.1

Patch release v4.47.1

We waited a little bit to make sure it was stable, thanks @​winglian for double checking and everyone for the fixes!

v4.47.0: PaliGemma-2, I-JEPA, OLMo-2, LayerSkip, Tensor Parallel

New models

PaliGemma-2

PaliGemma 2 and PaliGemma are lightweight open vision-language models (VLM) inspired by PaLI-3, and based on open components like the SigLIP vision model and the Gemma language model. PaliGemma takes both images and text as inputs and can answer questions about images with detail and context, meaning that PaliGemma can perform deeper analysis of images and provide useful insights, such as captioning for images and short videos, object detection, and reading text embedded within images.

PaliGemma 2 is available in 3B, 10B, and 28B parameter sizes, which are based on Gemma 2 2B, 9B, and 27B models, respectively. The original PaliGemma models are available in the 3B size. For more information on Gemma model variants, see the Gemma models list. PaliGemma model variants support different pixel resolutions for image inputs, including 224 x 224, 448 x 448, and 896 x 896 pixels.

I-JEPA

The I-JEPA model was proposed in Image-based Joint-Embedding Predictive Architecture by Mahmoud Assran, Quentin Duval, Ishan Misra, Piotr Bojanowski, Pascal Vincent, Michael Rabbat, Yann LeCun, Nicolas Ballas. I-JEPA is a self-supervised learning method that predicts the representations of one part of an image based on other parts of the same image. This approach focuses on learning semantic features without relying on pre-defined invariances from hand-crafted data transformations, which can bias specific tasks, or on filling in pixel-level details, which often leads to less meaningful representations.

OLMo 2

The OLMo2 model is the successor of the OLMo model, which was proposed in OLMo: Accelerating the Science of Language Models.

The architectural changes from the original OLMo model to this model are:

  • RMSNorm is used instead of standard layer norm.
  • Norm is applied to attention queries and keys.
  • Norm is applied after attention/feedforward layers rather than before.

... (truncated)

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@dependabot
Bump the pip-all-updates group with 7 updates
0da165d 
Bumps the pip-all-updates group with 7 updates:

| Package | From | To |
| --- | --- | --- |
| [coverage](https://github.com/nedbat/coveragepy) | `7.6.8` | `7.6.10` |
| [matplotlib](https://github.com/matplotlib/matplotlib) | `3.9.3` | `3.10.0` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.3.3` | `8.3.4` |
| [ruff](https://github.com/astral-sh/ruff) | `0.8.1` | `0.8.4` |
| [scikit-image](https://github.com/scikit-image/scikit-image) | `0.24.0` | `0.25.0` |
| [scikit-learn](https://github.com/scikit-learn/scikit-learn) | `1.5.2` | `1.6.0` |
| [transformers](https://github.com/huggingface/transformers) | `4.46.3` | `4.47.1` |


Updates `coverage` from 7.6.8 to 7.6.10
- [Release notes](https://github.com/nedbat/coveragepy/releases)
- [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst)
- [Commits](nedbat/coveragepy@7.6.8...7.6.10)

Updates `matplotlib` from 3.9.3 to 3.10.0
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](matplotlib/matplotlib@v3.9.3...v3.10.0)

Updates `pytest` from 8.3.3 to 8.3.4
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@8.3.3...8.3.4)

Updates `ruff` from 0.8.1 to 0.8.4
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.8.1...0.8.4)

Updates `scikit-image` from 0.24.0 to 0.25.0
- [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@v0.24.0...v0.25.0)

Updates `scikit-learn` from 1.5.2 to 1.6.0
- [Release notes](https://github.com/scikit-learn/scikit-learn/releases)
- [Commits](scikit-learn/scikit-learn@1.5.2...1.6.0)

Updates `transformers` from 4.46.3 to 4.47.1
- [Release notes](https://github.com/huggingface/transformers/releases)
- [Commits](huggingface/transformers@v4.46.3...v4.47.1)

---
updated-dependencies:
- dependency-name: coverage
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip-all-updates
- dependency-name: matplotlib
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip-all-updates
- dependency-name: pytest
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip-all-updates
- dependency-name: ruff
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip-all-updates
- dependency-name: scikit-image
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip-all-updates
- dependency-name: scikit-learn
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip-all-updates
- dependency-name: transformers
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip-all-updates
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Jan 1, 2025
@mmschlk mmschlk self-requested a review January 7, 2025 16:28
@mmschlk mmschlk merged commit 441b3b8 into main Jan 7, 2025
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@mmschlk mmschlk deleted the dependabot/pip/pip-all-updates-6f22e6b2c3 branch January 7, 2025 16:29
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