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Bump the python-packages group across 1 directory with 5 updates - #123

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Bumps the python-packages group with 5 updates in the / directory:

Package From To
polars 1.40.1 1.43.1
pot 0.9.6.post1 0.9.7
pycytominer 1.4.0 1.6.1
pytest 9.0.3 9.1.1
ruff 0.15.12 0.16.0

Updates polars from 1.40.1 to 1.43.1

Release notes

Sourced from polars's releases.

Python Polars 1.43.1

🚀 Performance improvements

  • Optimize not(bool_f) to not_bool_f (#28474)

✨ Enhancements

  • Allow callback sinks on cloud (#28458)

🐞 Bug fixes

  • Fix panic on self join of scan_delta / scan_iceberg (#28468)
  • Fix UB on first/last_non_null with empty chunk (#28495)
  • Do not CSE non-column height expr on streaming engine (#28480)
  • Propagate adjusted sortedness through Gather (#28493)
  • Deduplicate the expression equality checks (#28483)
  • Address 3VL issue with SQL NOT IN interaction with NULL values and joins (#28484)
  • Use total comparison in Expr literal values (#28482)
  • Ensure SQL SUM and CORR aggregates return NULL for all-null inputs, add TOTAL (#28475)
  • Share null_count_dtype helper between Delta and Iceberg, fixing SchemaError (#28479)
  • Remove non-output columns from the equi-join and semi/anti-join operators (#28446)
  • Fix dropped slice on multiple unions (#28477)
  • Fix in-memory engine incorrect slice on maintain order join (#28478)
  • Check join schema by position (#28455)
  • Block predicate pushdown past overwritten window keys (#28429)

📖 Documentation

  • Update and restructure README (#28490)
  • Minor fixes to Spark migration guide (#27730)
  • Relocate Polars Cloud & On-Prem User Guide (#28462)
  • Add notes on k8s operator (#28445)

🛠️ Other improvements

  • Make hive_part extraction a function and public (#28507)
  • Deduplicate the expression equality checks (#28483)
  • Bump ruff and mypy package versions (#28456)
  • Fix flaky test (#28454)

Thank you to all our contributors for making this release possible! @​AnirudhRahul, @​EndPositive, @​Jesse-Bakker, @​alexander-beedie, @​carnarez, @​dancsi, @​mdroogh, @​mroeschke, @​nameexhaustion, @​nchammas, @​orlp, @​r-brink and @​ritchie46

Python Polars 1.43.0

⚠️ Deprecations

  • Deprecate casting numeric types to categoricals (#28349)
  • Deprecate cat.get_categories() and cat.to_local() (#28299)
  • Deprecate LazyFrame.profile() (#28275)
  • Deprecate casts from non-nested dtypes into Lists (#28193)

... (truncated)

Commits
  • 8d438be Python Polars 1.43.1 (#28523)
  • a3e282a refactor: Make hive_part extraction a function and public (#28507)
  • f6d2bec docs: Update and restructure README (#28490)
  • b78761c feat(rust): Support reading IEEE 754 total order Parquet column order (#27896)
  • b1268f1 fix: Fix panic on self join of scan_delta / scan_iceberg (#28468)
  • 0d4a49a fix(rust): Decrement ParkGroup worker count when worker exits (#28492)
  • a3982dd fix(rust): Add missing Send bounds in Connector (#28497)
  • 49ceb73 fix: Fix UB on first/last_non_null with empty chunk (#28495)
  • 1f63626 fix: Do not CSE non-column height expr on streaming engine (#28480)
  • f75402e fix: Propagate adjusted sortedness through Gather (#28493)
  • Additional commits viewable in compare view

Updates pot from 0.9.6.post1 to 0.9.7

Release notes

Sourced from pot's releases.

0.9.7

This release contains several bug fixes and performance improvements, as well as updates to the documentation and examples and tests. We provide below a summary of the main new features and closed issues.

New exact OT solvers. This new release adds many new variants and updates for the exact OT solver. First a new lazy exact OT solver that re-computes distances on-the-fly from coordinates, reducing memory usage from O(n×m) to O(n+m) ( available in ot.solve_sample with lazy=True)). Another major feature is the addition of a warmstart feature for the EMD solver, allowing users to provide initial potentials to speed up convergence (with init_potentials in ot.solve and ot.solve_sample). Finally the release also include a sparse solver and ot.solve now accept sparse cost matrices and provides an OT plan whose support is included in the support of the cost matrix. All implementations are backend-agnostic and preserve gradient computation for automatic differentiation (but are solved on CPU).

The computational time for different solvers (on a laptop CPU) are shown below:

n 100 500 1000 5000
Solve 7.259e-04 1.501e-02 1.055e-01 2.343e+00
Solve Warm Start 6.970e-04 5.413e-03 2.291e-02 6.036e-01
Solve Lazy 1.280e-03 3.098e-02 1.421e-01 3.377e+00
Solve Sparse 10% 3.453e-04 6.716e-04 1.535e-03 3.534e-02

BSPOT solver. A new solver relying on Binary Space Partitioning (BSP) has been added to compute sparse transport plans between discrete measures in loglinear time which allows for very large problems to be solved. The release also includes a new ot.unbalanced.uot_1d solver with a Frank-Wolfe solver for unbalanced optimal transport in 1D.

Sliced OT pans Finally we now have a sliced OT plan solver that can be used to compute sliced transport plans (min-pivot sliced and expected sliced) between two measures.

OT between dynamical systems. A novel Spectral-Grassmann Wasserstein metric for operator representations of dynamical systems has been implemented in ot.sgot.

Unified API for barycenter solvers in ot.solve_bary_sample. A new free support solver for barycenter solvers has been added in ot.solve_bary_sample. You can see examples of how to use it here.

OT between high dimensional Gaussian distributions. New methods to compute the linear transport map and the related 2-Wasserstein distance between high-dimensional (HD) Gaussian distributions have been added in ot.gaussian.bures_wasserstein_mapping_hd and ot.gaussian.bures_wasserstein_distance_hd, respectively with empirical versions that estimate the distance from sample.

Batched solver for exact OT. The batch implementations have also been improved and you can now solve exact OT problems in parallel on CPU or GPU using the new proximal point solver in functions ot.solve_batch and ot.solve_sample_batch when reg=0 or no provided. A new batch loss for Fused unbalanced Gromov-Wasserstein is also now available in ot.batch.

New methods in unified API ot.solve_sample. The unified API function ot.solve_sample has also been updated to allows solving of specific problems such as BSP-OT, distance between high-dimensional (HD) Gaussian distributions and sliced and max-sliced distances.

Data normalization for sliced and ot.solve_sample solvers. The release also includes tools for data normalization and scaling which can not be used in sliced Wasserstein distance computations. A simple normalization class ot.utils.DataScaler has been added and supports all backends for 'standard', 'minmax', and 'l2' methods. Finally an optional scaler parameter has been added to ot.sliced_wasserstein_distance, ot.max_sliced_wasserstein_distance and ot.solve_sample.

New features

  • Refactor lazy EMD network simplex storage to avoid dense per-arc cost, endpoint, flow, and state storage where possible, and return sparse lazy transport plans instead of materializing dense plans internally (PR #813)
  • Removed OpenMP implementation in Simplex since no time gains are observed #820
  • Add sliced transport plans (min-pivot sliced and expected sliced) solvers (PR #767)
  • Add lazy EMD solver with on-the-fly distance computation from coordinates (PR #788)
  • Add Warmstart feature to the EMD solver for existing potentials (PR #793)
  • Add Warmstart potentials feature to the EMD solver for lazy and sparse solver (PR #795)
  • Faster init and result retrieval for EMD solver (PR #796)
  • Migrate backend from deprecated scipy.sparse.coo_matrix to modern scipy.sparse.coo_array (PR #782)
  • Geomloss function now handles both scalar and slice indices for i and j (PR #785)

... (truncated)

Changelog

Sourced from pot's changelog.

0.9.7

This release contains several bug fixes and performance improvements, as well as updates to the documentation and examples and tests. We provide below a summary of the main new features and closed issues.

New exact OT solvers. This new release adds many new variants and updates for the exact OT solver. First a new lazy exact OT solver that re-computes distances on-the-fly from coordinates, reducing memory usage from O(n×m) to O(n+m) ( available in ot.solve_sample with lazy=True)). Another major feature is the addition of a warmstart feature for the EMD solver, allowing users to provide initial potentials to speed up convergence (with init_potentials in ot.solve and ot.solve_sample). Finally the release also include a sparse solver and ot.solve now accept sparse cost matrices and provides an OT plan whose support is included in the support of the cost matrix. All implementations are backend-agnostic and preserve gradient computation for automatic differentiation (but are solved on CPU).

The computational time for different solvers (on a laptop CPU) are shown below:

n 100 500 1000 5000
Solve 7.259e-04 1.501e-02 1.055e-01 2.343e+00
Solve Warm Start 6.970e-04 5.413e-03 2.291e-02 6.036e-01
Solve Lazy 1.280e-03 3.098e-02 1.421e-01 3.377e+00
Solve Sparse 10% 3.453e-04 6.716e-04 1.535e-03 3.534e-02

BSPOT solver. A new solver relying on Binary Space Partitioning (BSP) has been added to compute sparse transport plans between discrete measures in loglinear time which allows for very large problems to be solved. The release also includes a new ot.unbalanced.uot_1d solver with a Frank-Wolfe solver for unbalanced optimal transport in 1D.

Sliced OT pans Finally we now have a sliced OT plan solver that can be used to compute sliced transport plans (min-pivot sliced and expected sliced) between two measures.

OT between dynamical systems. A novel Spectral-Grassmann Wasserstein metric for operator representations of dynamical systems has been implemented in ot.sgot.

Unified API for barycenter solvers in ot.solve_bary_sample. A new free support solver for barycenter solvers has been added in ot.solve_bary_sample. You can see examples of how to use it here.

OT between high dimensional Gaussian distributions. New methods to compute the linear transport map and the related 2-Wasserstein distance between high-dimensional (HD) Gaussian distributions have been added in ot.gaussian.bures_wasserstein_mapping_hd and ot.gaussian.bures_wasserstein_distance_hd, respectively with empirical versions that estimate the distance from sample.

Batched solver for exact OT. The batch implementations have also been improved and you can now solve exact OT problems in parallel on CPU or GPU using the new proximal point solver in functions ot.solve_batch and ot.solve_sample_batch when reg=0 or no provided. A new batch loss for Fused unbalanced Gromov-Wasserstein is also now available in ot.batch.

New methods in unified API ot.solve_sample. The unified API function ot.solve_sample has also been updated to allows solving of specific problems such as BSP-OT, distance between high-dimensional (HD) Gaussian distributions and sliced and max-sliced distances.

Data normalization for sliced and ot.solve_sample solvers. The release also includes tools for data normalization and scaling which can not be used in sliced Wasserstein distance computations. A simple normalization class ot.utils.DataScaler has been added and supports all backends for 'standard', 'minmax', and 'l2' methods. Finally an optional scaler parameter has been added to ot.sliced_wasserstein_distance, ot.max_sliced_wasserstein_distance and ot.solve_sample.

New features

  • Refactor lazy EMD network simplex storage to avoid dense per-arc cost, endpoint, flow, and state storage where possible, and return sparse lazy transport plans instead of materializing dense plans internally (PR #813)
  • Removed OpenMP implementation in Simplex since no time gains are observed #820
  • Add sliced transport plans (min-pivot sliced and expected sliced) solvers (PR #767)
  • Add lazy EMD solver with on-the-fly distance computation from coordinates (PR #788)
  • Add Warmstart feature to the EMD solver for existing potentials (PR #793)
  • Add Warmstart potentials feature to the EMD solver for lazy and sparse solver (PR #795)
  • Faster init and result retrieval for EMD solver (PR #796)
  • Migrate backend from deprecated scipy.sparse.coo_matrix to modern scipy.sparse.coo_array (PR #782)
  • Geomloss function now handles both scalar and slice indices for i and j (PR #785)

... (truncated)

Commits
  • a12794e [MRG] Release 0.9.7 (#829)
  • c980bda [MRG] Fix label-aware cost correction in ot.da (closes #664) (#833)
  • e52c2a3 [MRG] Proximal point solver for batched optimal transport (#832)
  • c836b97 [MRG] add debiasing and all new solvers to ot.solve_sample (#831)
  • 956240b Fixing issue in SGOT example and SGOT cost function. (#830)
  • f1e0c5c [MRG] Update wrapper for new geomloss version (#826)
  • 5a0f496 [MRG] Add backend-agnostic semi-discrete OT module and SGD-based solver in ot...
  • 60cbe12 [MRG] reorganize tests per backends (#828)
  • 6c98fac [MRG] Wrapper for OT barycenter solvers with free support (#730)
  • b74342c [MRG] Fix documentation for lowrank_sinkhorn and lowrank_gromov_wasserstein… ...
  • Additional commits viewable in compare view

Updates pycytominer from 1.4.0 to 1.6.1

Release notes

Sourced from pycytominer's releases.

v1.6.1 (2026-06-17)

Changes

v1.6.0 (2026-06-06)

Changes

v1.5.1 (2026-05-30)

What's Changed

Full Changelog: cytomining/pycytominer@v1.5.0...v1.5.1

v1.5.0 (2026-05-22)

What's Changed

... (truncated)

Commits

Updates pytest from 9.0.3 to 9.1.1

Release notes

Sourced from pytest's releases.

9.1.1

pytest 9.1.1 (2026-06-19)

Bug fixes

  • #14220: Fixed a logic bug in pytest.RaisesGroup which would might cause it to display incorrect "It matches FooError() which was paired with BarError" messages.
  • #14591: Fixed a regression in pytest 9.1.0 which caused overriding a parametrized fixture with an indirect @​pytest.mark.parametrize to fail with "duplicate parametrization of '<fixture name>'".
  • #14606: Fixed list-item typing errors from mypy in @pytest.mark.parametrize <pytest.mark.parametrize ref> argvalues parameter.
  • #14608: Fixed a regression in pytest 9.1.0 where conftest.py files located in <invocation dir>/test* were no longer loaded as initial conftests when invoked without arguments. This could cause certain hooks (like pytest_addoption) in these files to not fire.

9.1.0

pytest 9.1.0 (2026-06-13)

Removals and backward incompatible breaking changes

  • #14533: When using --doctest-modules, autouse fixtures with module, package or session scope that are defined inline in Python test modules (not plugins or conftests) will now possibly execute twice.

    If this is undesirable, move the fixture definition to a conftest.py file if possible.

    Technical explanation for those interested: When using --doctest-modules, pytest possibly collects Python modules twice, once as pytest.Module and once as a DoctestModule (depending on the configuration). Due to improvements in pytest's fixture implementation, if e.g. the DoctestModule collects a fixture, it is now visible to it only, and not to the Module. This means that both need to register the fixtures independently.

Deprecations (removal in next major release)

  • #10819: Added a deprecation warning for class-scoped fixtures defined as instance methods (without @classmethod). Such fixtures set attributes on a different instance than the test methods use, leading to unexpected behavior. Use @classmethod decorator instead -- by yastcher.

    See 10819 and 14011.

  • #12882: Calling request.getfixturevalue() <pytest.FixtureRequest.getfixturevalue> during teardown to request a fixture that was not already requested is now deprecated and will become an error in pytest 10.

    See dynamic-fixture-request-during-teardown for details.

  • #13409: Using non-~collections.abc.Collection iterables (such as generators, iterators, or custom iterable objects) for the argvalues parameter in @pytest.mark.parametrize <pytest.mark.parametrize ref> and metafunc.parametrize <pytest.Metafunc.parametrize> is now deprecated.

    These iterables get exhausted after the first iteration, leading to tests getting unexpectedly skipped in cases such as running pytest.main() multiple times, using class-level parametrize decorators, or collecting tests multiple times.

    See parametrize-iterators for details and suggestions.

  • #13946: The private config.inicfg attribute is now deprecated. Use config.getini() <pytest.Config.getini> to access configuration values instead.

    See config-inicfg for more details.

  • #14004: Passing baseid to ~pytest.FixtureDef or nodeid strings to fixture registration APIs is now deprecated. These are internal pytest APIs that are used by some plugins.

... (truncated)

Commits
  • cf470ec Prepare release version 9.1.1
  • e0c8ce6 Merge pull request #14625 from pytest-dev/patchback/backports/9.1.x/a07c31a97...
  • 1b82d16 Merge pull request #14624 from pytest-dev/patchback/backports/9.1.x/b375b79ec...
  • 501c4bc Merge pull request #14596 from bluetech/doc-classmethod
  • b61f588 Merge pull request #14622 from chrisburr/fix-14608-initial-conftest-test-subdir
  • 9a567e0 [automated] Update plugin list (#14617) (#14618)
  • ef8b299 Merge pull request #14620 from pytest-dev/patchback/backports/9.1.x/680f9f3ed...
  • 66abd07 Merge pull request #14220 from bysiber/fix-stale-iexp-raisesgroup
  • 79fbf93 Merge pull request #14612 from pytest-dev/patchback/backports/9.1.x/974ed48b6...
  • 0d312eb Merge pull request #14611 from bluetech/parametrize-argvalues-typing
  • Additional commits viewable in compare view

Updates ruff from 0.15.12 to 0.16.0

Release notes

Sourced from ruff's releases.

0.16.0

Release Notes

Released on 2026-07-23.

Check out the blog post for a migration guide and overview of the changes!

Breaking changes

  • Ruff now enables a much larger set of rules by default (413, up from 59). See the blog post for more details and the new Default Rules page for a full listing of the enabled rules. Note that this is primarily an expansion, but 18 of the more opinionated pycodestyle (E) and pyflakes (F) rules have been removed from the default set: E401, E402, E701, E702, E703, E711, E712, E713, E714, E721, E731, E741, E742, E743, F403, F405, F406, and F722.

  • Ruff can now format Python code blocks in Markdown files and will do this by default. See the documentation for more details.

  • Ruff now supports ruff: ignore comments at the ends of lines, like noqa comments, or on the line preceding a diagnostic. For example, these both suppress an unused-import (F401) diagnostic:

    import math  # ruff: ignore[F401]
ruff: ignore[F401]
import os

  • Fixes are now shown in check and format --check output:

    ❯ ruff format --check .
unformatted: File would be reformatted
 --> try.md:1:1
  |
1 | ```python
  - import   math
2 + import math
3 | ```
  |
1 file would be reformatted

    This example also shows off the Markdown formatting.

  • format --check now supports the same output formats as the linter, including the github and gitlab outputs for rendering annotations in CI:

    ❯ ruff format --check --output-format github .
::error title=ruff (unformatted),file=try.md,line=2,col=8,endLine=2,endColumn=10::try.md:2:8: unformatted: File would be reformatted

    See the CLI help or documentation for the full list of supported formats.

  • The filename, location, end_location, fix.edits[].location, and fix.edits[].end_location fields in the JSON output format may now be null rather than defaulting to the empty string and row 1, column 1, respectively.

... (truncated)

Changelog

Sourced from ruff's changelog.

0.16.0

Released on 2026-07-23.

Check out the blog post for a migration guide and overview of the changes!

Breaking changes

  • Ruff now enables a much larger set of rules by default (413, up from 59). See the blog post for more details and the new Default Rules page for a full listing of the enabled rules. Note that this is primarily an expansion, but 18 of the more opinionated pycodestyle (E) and pyflakes (F) rules have been removed from the default set: E401, E402, E701, E702, E703, E711, E712, E713, E714, E721, E731, E741, E742, E743, F403, F405, F406, and F722.

  • Ruff can now format Python code blocks in Markdown files and will do this by default. See the documentation for more details.

  • Ruff now supports ruff: ignore comments at the ends of lines, like noqa comments, or on the line preceding a diagnostic. For example, these both suppress an unused-import (F401) diagnostic:

    import math  # ruff: ignore[F401]
ruff: ignore[F401]
import os

  • Fixes are now shown in check and format --check output:

    ❯ ruff format --check .
unformatted: File would be reformatted
 --> try.md:1:1
  |
1 | ```python
  - import   math
2 + import math
3 | ```
  |
1 file would be reformatted

    This example also shows off the Markdown formatting.

  • format --check now supports the same output formats as the linter, including the github and gitlab outputs for rendering annotations in CI:

    

    • 






... (truncated)





Commits

    

  • a2635fd Bump 0.16.0 (#27136)
    • 

  • 3433449 [ty] Reuse full call diagnostics for implicit setter calls (#27115)
    • 

  • 2240070 Reflect ruff: ignore and --add-ignore stabilization in documentation (#27...
    • 

  • 17ef711 Stabilize --add-ignore (#27125)
    • 

  • ef912bb Add newly stabilized rules to defaults (#27055)
    • 

  • b30f040 Stabilize new default rules (#27035)
    • 

  • bcd70c5 Exclude Markdown files from format-dev runs (#27052)
    • 

  • 87e51e2 Fix format --check spans for syntax errors (#27045)
    • 

  • afe2723 [flake8-gettext] Stabilize qualified-name and built-in binding resolution (...
    • 

  • a9702d8 [flake8-bandit] Stabilize string literal binding resolution (S310) (#26944)
    • 

  • Additional commits viewable in compare view
    • 







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          Bump the python-packages group across 1 directory with 5 updates
        

          
                        
      


      

        

    
    
    

  

    


      


      

        

          

    
    
    

  

  

    
  



        

      


      

        
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Bumps the python-packages group with 5 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| [polars](https://github.com/pola-rs/polars) | `1.40.1` | `1.43.1` |
| [pot](https://github.com/PythonOT/POT) | `0.9.6.post1` | `0.9.7` |
| [pycytominer](https://github.com/cytomining/pycytominer) | `1.4.0` | `1.6.1` |
| [pytest](https://github.com/pytest-dev/pytest) | `9.0.3` | `9.1.1` |
| [ruff](https://github.com/astral-sh/ruff) | `0.15.12` | `0.16.0` |



Updates `polars` from 1.40.1 to 1.43.1
- [Release notes](https://github.com/pola-rs/polars/releases)
- [Commits](pola-rs/polars@py-1.40.1...py-1.43.1)

Updates `pot` from 0.9.6.post1 to 0.9.7
- [Release notes](https://github.com/PythonOT/POT/releases)
- [Changelog](https://github.com/PythonOT/POT/blob/master/RELEASES.md)
- [Commits](PythonOT/POT@0.9.6.post1...0.9.7)

Updates `pycytominer` from 1.4.0 to 1.6.1
- [Release notes](https://github.com/cytomining/pycytominer/releases)
- [Commits](cytomining/pycytominer@v1.4.0...v1.6.1)

Updates `pytest` from 9.0.3 to 9.1.1
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@9.0.3...9.1.1)

Updates `ruff` from 0.15.12 to 0.16.0
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.15.12...0.16.0)

---
updated-dependencies:
- dependency-name: polars
  dependency-version: 1.43.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: pot
  dependency-version: 0.9.7
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-packages
- dependency-name: pycytominer
  dependency-version: 1.6.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: pytest
  dependency-version: 9.1.1
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: ruff
  dependency-version: 0.16.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
...

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