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Updates the requirements on mypy, networkx, orbax-checkpoint, pydata-sphinx-theme, pygad, pytest-cov, rtree, ruff, sax and trame-vuetify to permit the latest version.
Updates mypy from 1.13.0 to 1.20.0

Changelog

Sourced from mypy's changelog.

Mypy Release Notes

Next Release

Mypy 1.20

We’ve just uploaded mypy 1.20.0 to the Python Package Index (PyPI). Mypy is a static type checker for Python. This release includes new features, performance improvements and bug fixes. You can install it as follows:

python3 -m pip install -U mypy

You can read the full documentation for this release on Read the Docs.

Planned Changes to Defaults and Flags in Mypy 2.0

As a reminder, we are planning to enable --local-partial-types by default in mypy 2.0, which will likely be the next feature release. This will often require at least minor code changes. This option is implicitly enabled by mypy daemon, so this makes the behavior of daemon and non-daemon modes consistent.

Note that this release improves the compatibility of --local-partial-types significantly to make the switch easier (see below for more).

This can also be configured in a mypy configuration file (use False to disable):

local_partial_types = True

For more information, refer to the documentation.

We will also enable --strict-bytes by default in mypy 2.0. This usually requires at most minor code changes to adopt. For more information, refer to the documentation.

Finally, --allow-redefinition-new will be renamed to --allow-redefinition. If you want to continue using the older --allow-redefinition semantics which are less flexible (e.g. limited support for conditional redefinitions), you can switch to --allow-redefinition-old, which is currently supported as an alias to the legacy --allow-redefinition behavior. To use --allow-redefinition in the upcoming mypy 2.0, you can't use --no-local-partial-types. For more information, refer to the documentation.

Better Type Narrowing

Mypy's implementation of narrowing has been substantially reworked. Mypy will now narrow more aggressively, more consistently, and more correctly. In particular, you are likely to notice new narrowing behavior in equality expressions (==), containment expressions (in),

... (truncated)

Commits
  • 770d3ca Remove +dev from version
  • 4738ffa Changelog updates for 1.20 (#21109)
  • b4f07a7 Use 'native-parser' instead of 'native-parse' for optional dependency (#21115)
  • 7bec7b7 [mypyc] Document librt and librt.base64 (#21114)
  • c482596 --allow-redefinition-new is no longer experimental (#21110)
  • c916ca3 sdist: include misc/{diff-cache,apply-cache-diff}.py for `mypy/test/test_di...
  • b137e4e [mypyc] Speed up native-to-native imports within the same group (#21101)
  • 978b711 [mypyc] Fix range loop variable off-by-one after loop exit (#21098)
  • 67ada30 [stubtest] Check runtime availability of private types not marked `@type_chec...
  • bdef6ef librt cache tests: build respecting MYPY_TEST_PREFIX (#21097)
  • Additional commits viewable in compare view

Updates networkx to 3.4.2

Release notes

Sourced from networkx's releases.

NetworkX 3.4.2

We're happy to announce the release of networkx 3.4.2!

Bug Fixes

  • Fix docstrings of dispatchable functions (#7679).
  • Fix draw_networkx_nodes return type (#7685).

Documentation

  • Add disclaimer about LLM driven PRs (#7683).

Maintenance

  • Fix doc warnings from recently added docs (#7682).

Contributors

6 authors added to this release (alphabetically):

4 reviewers added to this release (alphabetically):

These lists are automatically generated, and may not be complete or may contain duplicates.

Commits

Updates orbax-checkpoint to 0.11.33

Commits
  • 6a36d40 Increment Orbax version.
  • 0becf51 Update pytest command to use an ignore list from a YAML file.
  • 4cf67f6 Allow restore+broadcast logic to not require a single-replica sharding parame...
  • daec61e Normalize device kind strings when looking up HBM memory.
  • 46eea87 #v1 In-line CompositeHandler logic into Orbax Layouts
  • 53b2890 #v1 Strip down composite handler class and refactor functionality.
  • c339d50 Internal Change
  • cbdd63f #v1 Fork handler resolution functionality from composite_handler into resolut...
  • cf5a1ce Fix Pytree Metadata resolution and refactor V0 Layout logic
  • 2520b09 #p2p Support CPU memory ops in multislice functions
  • Additional commits viewable in compare view

Updates pydata-sphinx-theme to 0.17.0

Release notes

Sourced from pydata-sphinx-theme's releases.

v0.17.0

What's Changed

... (truncated)

Commits

Updates pygad from 3.3.1 to 3.5.0

Release notes

Sourced from pygad's releases.

PyGAD-3.5.0

  1. Fix a bug when minus sign (-) is used inside the stop_criteria parameter for multi-objective problems. ahmedfgad/GeneticAlgorithmPython#314 ahmedfgad/GeneticAlgorithmPython#323
  2. Fix a bug when the stop_criteria parameter is passed as an iterable (e.g. list) for multi-objective problems (e.g. ['reach_50_60', 'reach_20, 40']). ahmedfgad/GeneticAlgorithmPython#314
  3. Call the get_matplotlib() function from the plot_genes() method inside the pygad.visualize.plot.Plot class to import the matplotlib library. ahmedfgad/GeneticAlgorithmPython#315
  4. Create a new helper method called select_unique_value() inside the pygad/helper/unique.py script to select a unique gene from an array of values.
  5. Create a new helper method called get_random_mutation_range() inside the pygad/utils/mutation.py script that returns the random mutation range (min and max) for a single gene by its index.
  6. Create a new helper method called change_random_mutation_value_dtype inside the pygad/utils/mutation.py script that changes the data type of the value used to apply random mutation.
  7. Create a new helper method called round_random_mutation_value() inside the pygad/utils/mutation.py script that rounds the value used to apply random mutation.
  8. Create the pygad/helper/misc.py script with a class called Helper that has the following helper methods:
    1. change_population_dtype_and_round(): For each gene in the population, round the gene value and change the data type.
    2. change_gene_dtype_and_round(): Round the change the data type of a single gene.
    3. mutation_change_gene_dtype_and_round(): Decides whether mutation is done by replacement or not. Then it rounds and change the data type of the new gene value.
    4. validate_gene_constraint_callable_output(): Validates the output of the user-defined callable/function that checks whether the gene constraint defined in the gene_constraint parameter is satisfied or not.
    5. get_gene_dtype(): Returns the gene data type from the gene_type instance attribute.
    6. get_random_mutation_range(): Returns the random mutation range using the random_mutation_min_val and random_mutation_min_val instance attributes.
    7. get_initial_population_range(): Returns the initial population values range using the init_range_low and init_range_high instance attributes.
    8. generate_gene_value_from_space(): Generates/selects a value for a gene using the gene_space instance attribute.
    9. generate_gene_value_randomly(): Generates a random value for the gene. Only used if gene_space is None.
    10. generate_gene_value(): Generates a value for the gene. It checks whether gene_space is None and calls either generate_gene_value_randomly() or generate_gene_value_from_space().
    11. filter_gene_values_by_constraint(): Receives a list of values for a gene. Then it filters such values using the gene constraint.
    12. get_valid_gene_constraint_values(): Selects one valid gene value that satisfy the gene constraint. It simply calls generate_gene_value() to generate some gene values then it filters such values using filter_gene_values_by_constraint().
  9. Create a new helper method called mutation_process_random_value() inside the pygad/utils/mutation.py script that generates constrained random values for mutation. It calls either generate_gene_value() or get_valid_gene_constraint_values() based on whether the gene_constraint parameter is used or not.
  10. A new parameter called gene_constraint is added. It accepts a list of callables (i.e. functions) acting as constraints for the gene values. Before selecting a value for a gene, the callable is called to ensure the candidate value is valid. Check the [Gene Constraint](https://pygad.readthedocs.io/en/latest/pygad_more.html#gene-constraint) section for more information. ahmedfgad/GeneticAlgorithmPython#119
  11. A new parameter called sample_size is added. To select a gene value that respects a constraint, this variable defines the size of the sample from which a value is selected randomly. Useful if either allow_duplicate_genes or gene_constraint is used. An instance attribute of the same name is created in the instances of the pygad.GA class. Check the [sample_size Parameter](https://pygad.readthedocs.io/en/latest/pygad_more.html#sample-size-parameter) section for more information.
  12. Use the sample_size parameter instead of num_trials in the methods solve_duplicate_genes_randomly() and unique_float_gene_from_range() inside the pygad/helper/unique.py script. It is the maximum number of values to generate as the search space when looking for a unique float value out of a range.
  13. Fixed a bug in population initialization when allow_duplicate_genes=False. Previously, gene values were checked for duplicates before rounding, which could allow near-duplicates like 7.61 and 7.62 to pass. After rounding (e.g., both becoming 7.6), this resulted in unintended duplicates. The fix ensures gene values are now rounded before duplicate checks, preventing such cases.
  14. More tests are created.
  15. More examples are created.
  16. Edited the sort_solutions_nsga2() method in the pygad/utils/nsga2.py script to accept an optional parameter called find_best_solution when calling this method just to find the best solution.
  17. Fixed a bug while applying the non-dominated sorting in the get_non_dominated_set() method inside the pygad/utils/nsga2.py script. It was swapping the non-dominated and dominated sets. In other words, it used the non-dominated set as if it is the dominated set and vice versa. All the calls to this method were edited accordingly. ahmedfgad/GeneticAlgorithmPython#320.
  18. Fix a bug retrieving in the best_solution() method when retrieving the best solution for multi-objective problems. ahmedfgad/GeneticAlgorithmPython#331

PyGAD-3.4.0

  1. The delay_after_gen parameter is removed from the pygad.GA class constructor. As a result, it is no longer an attribute of the pygad.GA class instances. To add a delay after each generation, apply it inside the on_generation callback. ahmedfgad/GeneticAlgorithmPython#283
  2. In the single_point_crossover() method of the pygad.utils.crossover.Crossover class, all the random crossover points are returned before the for loop. This is by calling the numpy.random.randint() function only once before the loop to generate all the K points (where K is the offspring size). This is compared to calling the numpy.random.randint() function inside the for loop K times, once for each individual offspring.
  3. Bug fix in the examples/example_custom_operators.py script. ahmedfgad/GeneticAlgorithmPython#285
  4. While making prediction using the pygad.torchga.predict() function, no gradients are calculated.
  5. The gene_type parameter of the pygad.helper.unique.Unique.unique_int_gene_from_range() method accepts the type of the current gene only instead of the full gene_type list.
  6. Created a new method called unique_float_gene_from_range() inside the pygad.helper.unique.Unique class to find a unique floating-point number from a range.
  7. Fix a bug in the pygad.helper.unique.Unique.unique_gene_by_space() method to return the numeric value only instead of a NumPy array.
  8. Refactoring the pygad/helper/unique.py script to remove duplicate codes and reformatting the docstrings.
  9. The plot_pareto_front_curve() method added to the pygad.visualize.plot.Plot class to visualize the Pareto front for multi-objective problems. It only supports 2 objectives. ahmedfgad/GeneticAlgorithmPython#279
  10. Fix a bug converting a nested NumPy array to a nested list. ahmedfgad/GeneticAlgorithmPython#300
  11. The Matplotlib library is only imported when a method inside the pygad/visualize/plot.py script is used. This is more efficient than using import matplotlib.pyplot at the module level as this causes it to be imported when pygad is imported even when it is not needed. ahmedfgad/GeneticAlgorithmPython#292
  12. Fix a bug when minus sign (-) is used inside the stop_criteria parameter (e.g. stop_criteria=["saturate_10", "reach_-0.5"]). ahmedfgad/GeneticAlgorithmPython#296
  13. Make sure self.best_solutions is a list of lists inside the cal_pop_fitness method. ahmedfgad/GeneticAlgorithmPython#293
  14. Fix a bug where the cal_pop_fitness() method was using the previous_generation_fitness attribute to return the parents fitness. This instance attribute was not using the fitness of the latest population, instead the fitness of the population before the last one. The issue is solved by updating the previous_generation_fitness attribute to the latest population fitness before the GA completes. ahmedfgad/GeneticAlgorithmPython#291
Commits
  • 9ac7527 Merge pull request #334 from ahmedfgad/github-actions
  • 19250a9 Getting PyGAD 3.5.0 Ready
  • 83f0bed Merge pull request #333 from ahmedfgad/github-actions
  • eccdc6c Merge pull request #332 from ahmedfgad/master
  • a5ef680 Merge pull request #331 from Crylab/master
  • 9ac72f6 Clean repo
  • 3c7ed23 Solve a bug in NSGA2 tournament selection of parents
  • b2ac512 fix: keep original code + fix for multi-objective optimization
  • 7e068dd fix: best_solution for multi-objective optimization
  • c4e1164 Merge pull request #329 from ahmedfgad/master
  • Additional commits viewable in compare view

Updates pytest-cov to 7.1.0

Changelog

Sourced from pytest-cov's changelog.

7.1.0 (2026-03-21)

  • Fixed total coverage computation to always be consistent, regardless of reporting settings. Previously some reports could produce different total counts, and consequently can make --cov-fail-under behave different depending on reporting options. See [#641](https://github.com/pytest-dev/pytest-cov/issues/641) <https://github.com/pytest-dev/pytest-cov/issues/641>_.

  • Improve handling of ResourceWarning from sqlite3.

    The plugin adds warning filter for sqlite3 ResourceWarning unclosed database (since 6.2.0). It checks if there is already existing plugin for this message by comparing filter regular expression. When filter is specified on command line the message is escaped and does not match an expected message. A check for an escaped regular expression is added to handle this case.

    With this fix one can suppress ResourceWarning from sqlite3 from command line::

    pytest -W "ignore:unclosed database in <sqlite3.Connection object at:ResourceWarning" ...

  • Various improvements to documentation. Contributed by Art Pelling in [#718](https://github.com/pytest-dev/pytest-cov/issues/718) <https://github.com/pytest-dev/pytest-cov/pull/718>_ and "vivodi" in [#738](https://github.com/pytest-dev/pytest-cov/issues/738) <https://github.com/pytest-dev/pytest-cov/pull/738>. Also closed [#736](https://github.com/pytest-dev/pytest-cov/issues/736) <https://github.com/pytest-dev/pytest-cov/issues/736>.

  • Fixed some assertions in tests. Contributed by in Markéta Machová in [#722](https://github.com/pytest-dev/pytest-cov/issues/722) <https://github.com/pytest-dev/pytest-cov/pull/722>_.

  • Removed unnecessary coverage configuration copying (meant as a backup because reporting commands had configuration side-effects before coverage 5.0).

7.0.0 (2025-09-09)

  • Dropped support for subprocesses measurement.

    It was a feature added long time ago when coverage lacked a nice way to measure subprocesses created in tests. It relied on a .pth file, there was no way to opt-out and it created bad interations with coverage's new patch system <https://coverage.readthedocs.io/en/latest/config.html#run-patch>_ added in 7.10 <https://coverage.readthedocs.io/en/7.10.6/changes.html#version-7-10-0-2025-07-24>_.

    To migrate to this release you might need to enable the suprocess patch, example for .coveragerc:

    .. code-block:: ini

    [run] patch = subprocess

    This release also requires at least coverage 7.10.6.

  • Switched packaging to have metadata completely in pyproject.toml and use hatchling <https://pypi.org/project/hatchling/>_ for building. Contributed by Ofek Lev in [#551](https://github.com/pytest-dev/pytest-cov/issues/551) <https://github.com/pytest-dev/pytest-cov/pull/551>_ with some extras in [#716](https://github.com/pytest-dev/pytest-cov/issues/716) <https://github.com/pytest-dev/pytest-cov/pull/716>_.

  • Removed some not really necessary testing deps like six.

... (truncated)

Commits
  • 66c8a52 Bump version: 7.0.0 → 7.1.0
  • f707662 Make the examples use pypy 3.11.
  • 6049a78 Make context test use the old ctracer (seems the new sysmon tracer behaves di...
  • 8ebf20b Update changelog.
  • 861d30e Remove the backup context manager - shouldn't be needed since coverage 5.0, ...
  • fd4c956 Pass the precision on the nulled total (seems that there's some caching goion...
  • 78c9c4e Only run the 3.9 on older deps.
  • 4849a92 Punctuation.
  • 197c35e Update changelog and hopefully I don't forget to publish release again :))
  • 14dc1c9 Update examples to use 3.11 and make the adhoc layout example look a bit more...
  • Additional commits viewable in compare view

Updates rtree from 1.2.0 to 1.4.1

Release notes

Sourced from rtree's releases.

1.4.1b3

What's Changed

Full Changelog: Toblerity/rtree@1.4.1b1...1.4.1b3

1.4.1b1

What's Changed

New Contributors

Full Changelog: Toblerity/rtree@1.4.0...1.4.1b1

1.4.0

  • Python 3.9+ is now required (#321)
  • Add support for array-based bulk insert with NumPy (#340 by @​FreddieWitherden)
  • Upgrade binary wheels with libspatialindex-2.1.0 (#353)
  • Rename project and other build components to “rtree” (#350)

1.3.0

  • Upgrade binary wheels with libspatialindex-2.0.0 (#316)
  • Fix binary wheels for musllinux (#316)
  • Update code style, replace isort and black with ruff, modern numpy rng (#319)
  • Remove libsidx version testing (#313)
Changelog

Sourced from rtree's changelog.

1.4.1: 2025-08-13

  • Rename main branch references by :user:mwtoews in :PR:356
  • Fixing an incorrect reassignment in nearest_v and intersection_v by :user:Atilleusz in :PR:358
  • Add spatialindex version to tests, add common pytest configuration by :user:mwtoews in :PR:360
  • Refactor array-loading methods, add tests by :user:mwtoews in :PR:361
  • Minor refactor of code blocks in docs by :user:mwtoews in :PR:362
  • Resolve some issues in the batch API by :user:FreddieWitherden in :PR:367
  • fix #369 (load libspatialindex without changing cwd) by :user:remicres in :PR:370
  • arm64 wheels on windows by @​w8sl in :PR:378 and :PR:371

Full Changelog <https://github.com/Toblerity/rtree/compare/1.4.0...1.4.1>__

1.4.0: 2025-03-06

  • Python 3.9+ is now required (:PR:321)
  • Add support for array-based bulk insert with NumPy (:PR:340 by :user:FreddieWitherden)
  • Upgrade binary wheels with libspatialindex-2.1.0 (:PR:353)
  • Rename project and other build components to "rtree" (:PR:350)

1.3.0: 2024-07-10

  • Upgrade binary wheels with libspatialindex-2.0.0 (:PR:316)
  • Fix binary wheels for musllinux wheels (:PR:316)
  • Update code style, replace isort and black with ruff, modern numpy rng (:PR:319)
  • Remove libsidx version testing (:PR:313)
Commits

Updates ruff from 0.11.11 to 0.15.9

Release notes

Sourced from ruff's releases.

0.15.9

Release Notes

Released on 2026-04-02.

Preview features

  • [pyflakes] Flag annotated variable redeclarations as F811 in preview mode (#24244)
  • [ruff] Allow dunder-named assignments in non-strict mode for RUF067 (#24089)

Bug fixes

  • [flake8-errmsg] Avoid shadowing existing msg in fix for EM101 (#24363)
  • [flake8-simplify] Ignore pre-initialization references in SIM113 (#24235)
  • [pycodestyle] Fix W391 fixes for consecutive empty notebook cells (#24236)
  • [pyupgrade] Fix UP008 nested class matching (#24273)
  • [pyupgrade] Ignore strings with string-only escapes (UP012) (#16058)
  • [ruff] RUF072: skip formfeeds on dedent (#24308)
  • [ruff] Avoid re-using symbol in RUF024 fix (#24316)
  • [ruff] Parenthesize expression in RUF050 fix (#24234)
  • Disallow starred expressions as values of starred expressions (#24280)

Rule changes

  • [flake8-simplify] Suppress SIM105 for except* before Python 3.12 (#23869)
  • [pyflakes] Extend F507 to flag %-format strings with zero placeholders (#24215)
  • [pyupgrade] UP018 should detect more unnecessarily wrapped literals (UP018) (#24093)
  • [pyupgrade] Fix UP008 callable scope handling to support lambdas (#24274)
  • [ruff] RUF010: Mark fix as unsafe when it deletes a comment (#24270)

Formatter

  • Add nested-string-quote-style formatting option (#24312)

Documentation

  • [flake8-bugbear] Clarify RUF071 fix safety for non-path string comparisons (#24149)
  • [flake8-type-checking] Clarify import cycle wording for TC001/TC002/TC003 (#24322)

Other changes

  • Avoid rendering fix lines with trailing whitespace after | (#24343)

Contributors

... (truncated)

Changelog

Sourced from ruff's changelog.

0.15.9

Released on 2026-04-02.

Preview features

  • [pyflakes] Flag annotated variable redeclarations as F811 in preview mode (#24244)
  • [ruff] Allow dunder-named assignments in non-strict mode for RUF067 (#24089)

Bug fixes

  • [flake8-errmsg] Avoid shadowing existing msg in fix for EM101 (#24363)
  • [flake8-simplify] Ignore pre-initialization references in SIM113 (#24235)
  • [pycodestyle] Fix W391 fixes for consecutive empty notebook cells (#24236)
  • [pyupgrade] Fix UP008 nested class matching (#24273)
  • [pyupgrade] Ignore strings with string-only escapes (UP012) (#16058)
  • [ruff] RUF072: skip formfeeds on dedent (#24308)
  • [ruff] Avoid re-using symbol in RUF024 fix (#24316)
  • [ruff] Parenthesize expression in RUF050 fix (#24234)
  • Disallow starred expressions as values of starred expressions (#24280)

Rule changes

  • [flake8-simplify] Suppress SIM105 for except* before Python 3.12 (#23869)
  • [pyflakes] Extend F507 to flag %-format strings with zero placeholders (#24215)
  • [pyupgrade] UP018 should detect more unnece...

    Description has been truncated

    [!NOTE]
    Low Risk
    Only updates optional dependency pins/ranges; main risk is CI/lint/test behavior changes due to newer tool versions.

    Overview
    Dev/test/doc tooling dependency bumps in pyproject.toml, primarily widening/raising allowed versions.

    Updates include mypy (1.13.0→1.20.0), ruff (0.11.11→0.15.10), pygad (3.3.1→3.6.0), rtree (1.2.0→1.4.1), and relaxed upper bounds for packages like networkx (<3→<4), pytest-cov (<7→<8), pydata-sphinx-theme (<0.16→<0.18), sax (<0.12→<0.15), orbax-checkpoint (<0.11.33→<0.11.35), and trame-vuetify (<3→<4) across relevant optional dependency groups.

    Reviewed by Cursor Bugbot for commit ebe9d2f. Bugbot is set up for automated code reviews on this repo. Configure here.

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@dependabot
chore(deps-dev): bump the python group across 1 directory with 10 upd…
ebe9d2f 
…ates

Updates the requirements on [mypy](https://github.com/python/mypy), [networkx](https://github.com/networkx/networkx), [orbax-checkpoint](https://github.com/google/orbax), [pydata-sphinx-theme](https://github.com/pydata/pydata-sphinx-theme), [pygad](https://github.com/ahmedfgad/GeneticAlgorithmPython), [pytest-cov](https://github.com/pytest-dev/pytest-cov), [rtree](https://github.com/Toblerity/rtree), [ruff](https://github.com/astral-sh/ruff), [sax](https://github.com/flaport/sax) and [trame-vuetify](https://github.com/Kitware/trame-vuetify) to permit the latest version.

Updates `mypy` from 1.13.0 to 1.20.0
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.13.0...v1.20.0)

Updates `networkx` to 3.4.2
- [Release notes](https://github.com/networkx/networkx/releases)
- [Commits](networkx/networkx@networkx-2.6.3...networkx-3.4.2)

Updates `orbax-checkpoint` to 0.11.33
- [Release notes](https://github.com/google/orbax/releases)
- [Changelog](https://github.com/google/orbax/blob/main/CHANGELOG.md)
- [Commits](google/orbax@v0.0.0...v0.11.33)

Updates `pydata-sphinx-theme` to 0.17.0
- [Release notes](https://github.com/pydata/pydata-sphinx-theme/releases)
- [Changelog](https://github.com/pydata/pydata-sphinx-theme/blob/main/RELEASE.md)
- [Commits](pydata/pydata-sphinx-theme@v0.13.3...v0.17.0)

Updates `pygad` from 3.3.1 to 3.5.0
- [Release notes](https://github.com/ahmedfgad/GeneticAlgorithmPython/releases)
- [Commits](ahmedfgad/GeneticAlgorithmPython@3.3.1...3.5.0)

Updates `pytest-cov` to 7.1.0
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](pytest-dev/pytest-cov@v6.0.0...v7.1.0)

Updates `rtree` from 1.2.0 to 1.4.1
- [Release notes](https://github.com/Toblerity/rtree/releases)
- [Changelog](https://github.com/Toblerity/rtree/blob/main/CHANGES.rst)
- [Commits](Toblerity/rtree@1.2.0...1.4.1)

Updates `ruff` from 0.11.11 to 0.15.9
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.11.11...0.15.9)

Updates `sax` to 0.14.2
- [Release notes](https://github.com/flaport/sax/releases)
- [Changelog](https://github.com/flaport/sax/blob/main/CHANGELOG.md)
- [Commits](flaport/sax@0.11.0...0.14.2)

Updates `trame-vuetify` to 3.2.1
- [Release notes](https://github.com/Kitware/trame-vuetify/releases)
- [Changelog](https://github.com/Kitware/trame-vuetify/blob/master/CHANGELOG.md)
- [Commits](Kitware/trame-vuetify@v2.0.1...v3.2.1)

---
updated-dependencies:
- dependency-name: mypy
  dependency-version: 1.20.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python
- dependency-name: networkx
  dependency-version: 3.4.2
  dependency-type: direct:development
  dependency-group: python
- dependency-name: orbax-checkpoint
  dependency-version: 0.11.33
  dependency-type: direct:development
  dependency-group: python
- dependency-name: pydata-sphinx-theme
  dependency-version: 0.17.0
  dependency-type: direct:development
  dependency-group: python
- dependency-name: pygad
  dependency-version: 3.5.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python
- dependency-name: pytest-cov
  dependency-version: 7.1.0
  dependency-type: direct:development
  dependency-group: python
- dependency-name: rtree
  dependency-version: 1.4.1
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python
- dependency-name: ruff
  dependency-version: 0.15.9
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python
- dependency-name: sax
  dependency-version: 0.14.2
  dependency-type: direct:development
  dependency-group: python
- dependency-name: trame-vuetify
  dependency-version: 3.2.1
  dependency-type: direct:development
  dependency-group: python
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot force-pushed the dependabot/pip/python-894410e37c branch from 3465260 to ebe9d2f Compare April 16, 2026 18:10
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