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chore(deps): bump the routine group with 8 updates - #144

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chore(deps): bump the routine group with 8 updates#144
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Bumps the routine group with 8 updates:

Package From To
pyside6 6.5.2 6.11.2
vtk 9.3.1 9.7.0
scipy 1.14.1 1.17.1
scikit-image 0.23.2 0.26.0
shapely 2.1.1 2.1.2
numcodecs 0.15.0 0.16.5
lxml 6.1.0 6.1.2
gitpython 3.1.59 3.1.61

Updates pyside6 from 6.5.2 to 6.11.2

Updates vtk from 9.3.1 to 9.7.0

Updates scipy from 1.14.1 to 1.17.1

Release notes

Sourced from scipy's releases.

SciPy 1.17.1 Release Notes

SciPy 1.17.1 is a bug-fix release with no new features compared to 1.17.0.

Authors

  • Name (commits)
  • Evgeni Burovski (5)
  • Lucas Colley (1)
  • Christoph Gohlke (1)
  • Ralf Gommers (6)
  • Matt Haberland (5)
  • Matthias Koeppe (1)
  • Nick ODell (1)
  • Ilhan Polat (10)
  • Tyler Reddy (44)
  • Martin Schuck (3)
  • Dan Schult (3)
  • stratakis (1) +
  • ਗਗਨਦੀਪ ਸਿੰਘ (Gagandeep Singh) (1)

A total of 13 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.

Complete issue list, PR list, and release asset hashes are available in the associated README.txt.

SciPy 1.17.0 Release Notes

SciPy 1.17.0 is the culmination of 6 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Before upgrading, we recommend that users check that their own code does not use deprecated SciPy functionality (to do so, run your code with python -Wd and check for DeprecationWarning s). Our development attention will now shift to bug-fix releases on the 1.17.x branch, and on adding new features on the main branch.

This release requires Python 3.11-3.14 and NumPy 1.26.4 or greater.

Highlights of this release

  • Many SciPy functions have gained native support for batching of N-dimensional array input and additional support for the array API standard. An overall

... (truncated)

Commits
  • 527eb7f REL: 1.17.1 release commit [wheel build]
  • f11663b Merge pull request #24584 from tylerjereddy/treddy_prep_1.17.1
  • 2c49e68 DOC: PR 24584 revisions
  • 400fa15 safely convert index dtypes to intc for csgraph and superLU
  • 8c70404 MAINT: PR 24584 revisions [wheel build]
  • 6dda8c1 BUG: PR 24584 revisions
  • 4a187e5 DOC: PR 24584 revisions
  • 463ee9f ENH: linalg/inv: re-enable overwrite_a for 2D inputs (#24442)
  • df746ee BUG: linalg: restore dtypes in inv, solve, det
  • 246bfee MAINT:optimize: Enable multi-phase init to DIRECT
  • Additional commits viewable in compare view

Updates scikit-image from 0.23.2 to 0.26.0

Release notes

Sourced from scikit-image's releases.

v0.26.0

scikit-image 0.26.0

We're happy to announce the release of scikit-image 0.26.0!

New Features

  • Add new parameter max_step_cost to skimage.graph.MCP.find_costs which allows limiting the maximal stepping cost between points (#7625).
  • In skimage.transform, add the identity class constructor to all geometric transforms. For example, you can now use skimage.transform.PolynomialTransform(dimensionality=2) (#7754).
  • Add new property intensity_median to skimage.measure.regionprops (#7745).
  • binary_blobs now supports a mode parameter for the Gaussian filter, allowing periodic boundary conditions with mode="wrap" (#7909).

API Changes

  • In skimage.morphology, deprecate binary_erosion, binary_dilation, binary_opening, and binary_closing in favor of erosion, dilation, opening, and closing respectively. The binary versions weren't actually significantly faster than their non-binary counterparts and sometimes significantly slower. In the future, we might add optimizations internally to the remaining (general, non-binary) functions for when they're used with binary inputs (#7665).
  • Deprecate parameter max_cost in skimage.graph.MCP.find_costs which previously did nothing. Use the new parameter max_step_cost instead (#7625).
  • Deprecate parameter max_cumulative_cost in skimage.graph.MCP.find_costs which did nothing (#7625).
  • In skimage.morphology.remove_small_objects, deprecate the min_size parameter in favor of the new max_size parameter to make API and behavior clearer. This new threshold removes objects smaller than or equal to its value, while the previous parameter only removed smaller ones (#7739).
  • In skimage.morphology.remove_small_holes, deprecate the area_threshold parameter in favor of the new max_size parameter to make API and behavior clearer. This new threshold removes holes smaller than or equal to its value, while the previous parameter only removed smaller ones (#7739).
  • In skimage.transform, deprecate the use of scalar scale, with dimensionality=3 where this can be passed to a geometric transform contructor. This allows us to generalize the use of the constructors to the case where the parameters must specify the dimensionality, unless you mean to construct an identity transform (#7754).
  • In skimage.transform, turn all input parameters to transform constructors keyword-only (other than matrix). This avoids confusion due to the positional parameter order being different from the order by which they are applied in AffineTransform (#7754).
  • Deprecate parameter num_threads in skimage.restoration.rolling_ball; use workers instead (#7302).
  • Deprecate parameter num_workers in skimage.restoration.cycle_spin; use workers instead (#7302).
  • Officially deprecate old properties in skimage.measure.regionprops and related functions. While we removed the documentation for these some time ago, they where still accessible as keys (via __get_item__) or attributes. Going forward, using deprecated keys or attributes, will emit an appropriate warning (#7778).
  • In skimage.measure, add a new class method and constructor from_estimate for LineModelND, CircleModel, and EllipseModel. This replaces the old API—the now deprecated estimate method—which required initalizing a model with undefined parameters before calling estimate (#7771).
  • In skimage.transform, add a new class method and constructor from_estimate for AffineTransform, EssentialMatrixTransform, EuclideanTransform, FundamentalMatrixTransform, PiecewiseAffineTransform, PolynomialTransform, ProjectiveTransform, SimilarityTransform, and ThinPlateSplineTransform. This replaces the old API—the now deprecated estimate method—which required initializing an undefined transform before calling estimate (#7771).
  • Deprecate skimage.measure.fit.BaseModel; after we expire the other *Model* deprecations, there is no work for an ancestor class to do (#7789).
  • In skimage.measure, deprecate .params attributes of the models CircleModel, EllipseModel, and LineModelND. Instead set model-specific attributes: origin, direction for LineModelND; center, radius for CircleModel, center, ax_lens, theta for EllipseModel (#7789).
  • In skimage.measure, deprecate use of model constructor calls without arguments leaving an uninitialized instance (for example CircleModel()). This applies to CircleModel, EllipseModel, and LineModelND. Instead prefer input arguments to define instances (for example CircleModel(center, radius)). This follows on from prior deprecation of the estimate method, which had implied the need for the no-argument constructor, of form cm = CircleMoldel(); cm.estimate(data) (#7789).
  • In skimage.measure, deprecate use of params arguments to predict* calls of model objects. This applies to CircleModel, EllipseModel, and LineModelND. We now ask instead that the user provide initialization equivalent to the params content in the class construction. For example, prefer cm = CircleModel((2, 3), 4); x = cm.predict_x(t) to cm = CircleMoldel(); x = cm.predict_x(t, params=(2, 3, 4))) (#7789).

Enhancements

  • Raise a ValueError instead of a TypeError in CircleModel, EllipseModel, and LineModelND in skimage.measure. This applies when failing to pass a value for params (or passing params=None) to predict methods of an uninitialized transform (#7789).
  • In skimage.measure, the RegionProperties class that is returned by regionprops, now has a formatted string representation (__repr__). This representation includes the label of the region and its bounding box (#7887).

Performance

  • Use greedy einsum optimization in skimage.measure.moments_central (#7947).
  • Add lazy loading to skimage.segmentation (#7035).

Bug Fixes

  • Make deconvolution example scientifically sensible (#7589).
  • In skimage.filters.sobel/scharr/prewitt/farid, when mode="constant" is used ensure that cval has an effect. It didn't previously (#7826).
  • Ensure skimage.graph.cut_normalized is deterministic when seeded with the rng parameter and when SciPy 1.17.0.dev0 or newer is installed. With earlier SciPy versions the internally used function scipy.linalg.eigsh is not deterministic and can lead to different results (#7912).
  • Avoid potential integer overflow in skimage.morphology.reconstruction (#7938).
  • Handle negative axis lengths due to numerical errors in axis_major_length and axis_minor_length properties of skimage.measure.regionprops (#7916).
  • In skimage.util.random_noise, ensure that clip argument is handled consistently for various modes (#7924).
  • Apparent fix for Hough transform stray j (#7974).

... (truncated)

Commits
  • ee0a7a3 Designate 0.26.0 release
  • b0e3c2d Clarify RELEASE.txt after v0.26.0rc2 (#7990)
  • a12ddfa Bump version in skimage init to 0.26.0rc3.dev0
  • ab3bd14 Bump version in skimage init to 0.26.0rc2
  • c27ac8f Designate 0.26.0rc2 release (#7987)
  • 211223b Clarify non-native support for masked array in the documentation (#7968)
  • b3da953 Mark test_wrap_around as xfail on macOS until 2026-02-01 (#7985)
  • 2799d12 Note issue number tracking the flakiness
  • 52996fd Set exception type in xfail
  • dd49f1f xfail on macOS and make mark temporary until 2026-02-01
  • Additional commits viewable in compare view

Updates shapely from 2.1.1 to 2.1.2

Release notes

Sourced from shapely's releases.

2.1.2

Wheels are available for Python 3.14 (and still include GEOS 3.13.1).

Changelog

Sourced from shapely's changelog.

2.1.2 (2025-09-24)

Wheels are available for Python 3.14 (and still include GEOS 3.13.1).

Commits
  • 5fb639d RLS: 2.1.2
  • 70509a1 DOC/RLS: indicate Python 3.14 support in pyproject.toml and release notes for...
  • 5c572b6 CI: add testing with GEOS 3.14 and Python 3.14 (#2330)
  • a909333 Bump pypa/cibuildwheel from 3.1.3 to 3.2.0 (#2328)
  • 2086d44 Bump actions/setup-python from 5 to 6 (#2326)
  • 50c1cf3 Bump actions/download-artifact from 4 to 5 (#2321)
  • 39490ab TST: update test_coverage_union_overlapping_inputs for upstream GEOS change (...
  • 5ef437c Bump actions/checkout from 4 to 5 (#2320)
  • 7b5ff3d BLD: add Python 3.14 wheels [Bump pypa/cibuildwheel from 3.0.1 to 3.1.3] (#2316)
  • 480dbb1 TST: update frechet_distance densify test for latest GEOS main (densify>0.001...
  • Additional commits viewable in compare view

Updates numcodecs from 0.15.0 to 0.16.5

Release notes

Sourced from numcodecs's releases.

v0.16.5

What's Changed

Full Changelog: zarr-developers/numcodecs@v0.16.4...v0.16.5

v0.16.4

What's Changed

New Contributors

Full Changelog: zarr-developers/numcodecs@v0.16.3...v0.16.4

0.16.3

What's Changed

Full Changelog: zarr-developers/numcodecs@v0.16.2...v0.16.3

v0.16.2

What's Changed

... (truncated)

Changelog

Sourced from numcodecs's changelog.

0.16.5

Fixes

  • Restore prior optional dependency behavior for 'crc32c' group. By {user}Davis Bennett <d-v-b>, {issue}802

(release_0.16.4)=

0.16.4

Enhancements

  • The Zstandard codec can now decode bytes containing multiple frames. By {user}Mark Kittisopikul <mkitti>, {issue}757

  • Add Python 3.14 support to the test matrix. By {user}Max Jones <maxrjones>, {issue}799

  • Add Python 3.14 wheel builds. By {user}Davis Bennett <d-v-b>, {issue}796

Fixes

  • Fix PCodec.decode() to handle numpy arrays by calling ensure_bytes on input buffers. By {user}Sam Levang <slowjazz>, {issue}756

Maintenance

  • Replace crc32c dependency with google-crc32c. By {user}Joe Hamman <jhamman>, {issue}792

  • Refactor numcodecs.zarr3 to re-export classes from zarr.codecs._numcodecs instead of defining them locally. By {user}Davis Bennett <d-v-b>, {issue}780

  • Add testing against zarr-python main branch. By {user}Max Jones <maxrjones>, {issue}800

  • Add pcodec and zfpy to 32-bit CI testing. By {user}Mark Kittisopikul <mkitti>, {issue}786

  • Improve CRC32C codec test skipping to properly report skipped tests using pytest.skipif. By {user}Agriya Khetarpal <agriyakhetarpal>, {issue}740

  • Add nightly wheel upload to scientific-python channel. By {user}Ian Hunt-Isaak <ianhi>, {issue}787

  • Fetch tags to version nightly wheels correctly. By {user}Ian Hunt-Isaak <ianhi>, {issue}790

... (truncated)

Commits

Updates lxml from 6.1.0 to 6.1.2

Changelog

Sourced from lxml's changelog.

6.1.2 (2026-08-18)

  • GH#526: Some build files were missing in the sdist. Patch by Nicola Soranzo.

  • Some minor corrections for error handling cases.

Other changes

  • Built with Cython 3.2.9.

6.1.1 (2026-05-18)

Bugs fixed

Commits
  • f2874e9 Update release date.
  • 687a295 Build: Exclude Py3.8 from windows-arm builds.
  • acadc56 Build: Remove outdated build target.
  • 59f93eb Build: Split old-Linux and other-Py3.8 builds.
  • 923df83 Build: Fix manylinux2014 build.
  • 975cc83 Build: Fix Px3.8 build setup.
  • 09e5d3e Build: Fix cibuildwheel version.
  • 998cf50 Build: Build Py3.8 wheels only once, not in every build job.
  • 5567037 Build: Exclude Py3.15 from 32bit builds.
  • 904db40 Build: Update cibuildwheel to include Py3.15.
  • Additional commits viewable in compare view

Updates gitpython from 3.1.59 to 3.1.61

Release notes

Sourced from gitpython's releases.

3.1.61

Fix accidental removal of exploitable regex in Actor by bringing it back, and deprecating it.

What's Changed

New Contributors

Full Changelog: gitpython-developers/GitPython@3.1.60...3.1.61

3.1.60 Security

What's Changed

Full Changelog: gitpython-developers/GitPython@3.1.59...3.1.60

Commits
  • 5346d1b prepare next release
  • d81336b Merge pull request #2221 from gitpython-developers/re-add-regex
  • bc63b02 fix: restore Actor.name_email_regex (#2220)
  • a9fb008 Merge pull request #2219 from Vogtinator/main
  • db1a2cf fix: wait for git daemon to listen before connecting
  • 3481da9 Merge pull request #2218 from gitpython-developers/fix-repo-open
  • 56636c3 prepare new release
  • c7cf4d1 fix: prefer .git during repository discovery
  • d160fb4 Merge pull request #2217 from gitpython-developers/fix-advisory
  • 09f2cf3 fix: require opt-in for no-index diffs
  • Additional commits viewable in compare view

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@dependabot
chore(deps): bump the routine group with 8 updates
0f40445 
Bumps the routine group with 8 updates:

| Package | From | To |
| --- | --- | --- |
| [pyside6](https://pyside.org) | `6.5.2` | `6.11.2` |
| [vtk](https://vtk.org) | `9.3.1` | `9.7.0` |
| [scipy](https://github.com/scipy/scipy) | `1.14.1` | `1.17.1` |
| [scikit-image](https://github.com/scikit-image/scikit-image) | `0.23.2` | `0.26.0` |
| [shapely](https://github.com/shapely/shapely) | `2.1.1` | `2.1.2` |
| [numcodecs](https://github.com/zarr-developers/numcodecs) | `0.15.0` | `0.16.5` |
| [lxml](https://github.com/lxml/lxml) | `6.1.0` | `6.1.2` |
| [gitpython](https://github.com/gitpython-developers/GitPython) | `3.1.59` | `3.1.61` |


Updates `pyside6` from 6.5.2 to 6.11.2

Updates `vtk` from 9.3.1 to 9.7.0

Updates `scipy` from 1.14.1 to 1.17.1
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.14.1...v1.17.1)

Updates `scikit-image` from 0.23.2 to 0.26.0
- [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@v0.23.2...v0.26.0)

Updates `shapely` from 2.1.1 to 2.1.2
- [Release notes](https://github.com/shapely/shapely/releases)
- [Changelog](https://github.com/shapely/shapely/blob/main/CHANGES.txt)
- [Commits](shapely/shapely@2.1.1...2.1.2)

Updates `numcodecs` from 0.15.0 to 0.16.5
- [Release notes](https://github.com/zarr-developers/numcodecs/releases)
- [Changelog](https://github.com/zarr-developers/numcodecs/blob/main/docs/release.md)
- [Commits](zarr-developers/numcodecs@v0.15.0...v0.16.5)

Updates `lxml` from 6.1.0 to 6.1.2
- [Release notes](https://github.com/lxml/lxml/releases)
- [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt)
- [Commits](lxml/lxml@lxml-6.1.0...lxml-6.1.2)

Updates `gitpython` from 3.1.59 to 3.1.61
- [Release notes](https://github.com/gitpython-developers/GitPython/releases)
- [Changelog](https://github.com/gitpython-developers/GitPython/blob/main/CHANGES)
- [Commits](gitpython-developers/GitPython@3.1.59...3.1.61)

---
updated-dependencies:
- dependency-name: pyside6
  dependency-version: 6.11.2
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: routine
- dependency-name: vtk
  dependency-version: 9.7.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: routine
- dependency-name: scipy
  dependency-version: 1.17.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: routine
- dependency-name: scikit-image
  dependency-version: 0.26.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: routine
- dependency-name: shapely
  dependency-version: 2.1.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: routine
- dependency-name: numcodecs
  dependency-version: 0.16.5
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: routine
- dependency-name: lxml
  dependency-version: 6.1.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: routine
- dependency-name: gitpython
  dependency-version: 3.1.61
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: routine
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot Bot added dependencies Pull requests that update a dependency file python Pull requests that update python code labels Sep 1, 2026
@dependabot
dependabot Bot requested a review from quasiTriestino as a code owner September 1, 2026 16:54
@dependabot dependabot Bot added dependencies Pull requests that update a dependency file python Pull requests that update python code labels Sep 1, 2026
@github-actions
github-actions Bot merged commit b053b1d into main Sep 1, 2026
2 checks passed
@github-actions
github-actions Bot deleted the dependabot/pip/routine-d571c40229 branch September 1, 2026 16:54
dustenhubbard added a commit that referenced this pull request Sep 1, 2026
@dustenhubbard
fix(deps): restore the pre-#144 pins so main installs (#151)
c454ba0 
#144 merged with its tests red. The bump raised scipy to 1.17.1 and left numpy
at 1.24.1, but scipy 1.17.1 needs numpy >=1.26.4, so the package cannot be
installed at all:

    ERROR: Cannot install pyreconstruct because these package versions have
    conflicting dependencies.
        pyreconstruct depends on numpy==1.24.1
        scipy 1.17.1 depends on numpy<2.7 and >=1.26.4

Every open dependency PR branches off main and fails the same way, whatever it
changes. This puts all eight pins back to the set CI last passed on. I will
bring the bumps back in pieces, starting with numpy.
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