build(deps): bump the python-packages group across 1 directory with 1…

…3 updates; retain cytominer-database 0.3.4 (#473)

* build(deps): bump the python-packages group across 1 directory with 13 updates

Bumps the python-packages group with 13 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| [scikit-learn](https://github.com/scikit-learn/scikit-learn) | `1.5.0` | `1.5.2` |
| [boto3](https://github.com/boto/boto3) | `1.34.51` | `1.35.36` |
| [fire](https://github.com/google/python-fire) | `0.6.0` | `0.7.0` |
| [cytominer-database](https://github.com/cytomining/cytominer-database) | `0.3.4` | `0.3.5` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.1.1` | `8.3.3` |
| [commitizen](https://github.com/commitizen-tools/commitizen) | `3.20.0` | `3.30.0` |
| [ruff](https://github.com/astral-sh/ruff) | `0.3.4` | `0.7.2` |
| [mypy](https://github.com/python/mypy) | `1.11.2` | `1.13.0` |
| [mkdocs](https://github.com/mkdocs/mkdocs) | `1.5.3` | `1.6.1` |
| [sphinx-autoapi](https://github.com/readthedocs/sphinx-autoapi) | `3.0.0` | `3.3.3` |
| [ipython](https://github.com/ipython/ipython) | `8.12.3` | `8.18.0` |
| [nbsphinx](https://github.com/spatialaudio/nbsphinx) | `0.9.3` | `0.9.5` |
| [dunamai](https://github.com/mtkennerly/dunamai) | `1.19.2` | `1.22.0` |



Updates `scikit-learn` from 1.5.0 to 1.5.2
- [Release notes](https://github.com/scikit-learn/scikit-learn/releases)
- [Commits](scikit-learn/scikit-learn@1.5.0...1.5.2)

Updates `boto3` from 1.34.51 to 1.35.36
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](boto/boto3@1.34.51...1.35.36)

Updates `fire` from 0.6.0 to 0.7.0
- [Release notes](https://github.com/google/python-fire/releases)
- [Commits](google/python-fire@v0.6.0...v0.7.0)

Updates `cytominer-database` from 0.3.4 to 0.3.5
- [Release notes](https://github.com/cytomining/cytominer-database/releases)
- [Commits](cytomining/cytominer-database@v0.3.4...v0.3.5)

Updates `pytest` from 8.1.1 to 8.3.3
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@8.1.1...8.3.3)

Updates `commitizen` from 3.20.0 to 3.30.0
- [Release notes](https://github.com/commitizen-tools/commitizen/releases)
- [Changelog](https://github.com/commitizen-tools/commitizen/blob/master/CHANGELOG.md)
- [Commits](commitizen-tools/commitizen@v3.20.0...v3.30.0)

Updates `ruff` from 0.3.4 to 0.7.2
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@v0.3.4...0.7.2)

Updates `mypy` from 1.11.2 to 1.13.0
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.11.2...v1.13.0)

Updates `mkdocs` from 1.5.3 to 1.6.1
- [Release notes](https://github.com/mkdocs/mkdocs/releases)
- [Commits](mkdocs/mkdocs@1.5.3...1.6.1)

Updates `sphinx-autoapi` from 3.0.0 to 3.3.3
- [Release notes](https://github.com/readthedocs/sphinx-autoapi/releases)
- [Changelog](https://github.com/readthedocs/sphinx-autoapi/blob/main/CHANGELOG.rst)
- [Commits](readthedocs/sphinx-autoapi@v3.0.0...v3.3.3)

Updates `ipython` from 8.12.3 to 8.18.0
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](ipython/ipython@8.12.3...8.18.0)

Updates `nbsphinx` from 0.9.3 to 0.9.5
- [Release notes](https://github.com/spatialaudio/nbsphinx/releases)
- [Changelog](https://github.com/spatialaudio/nbsphinx/blob/master/NEWS.rst)
- [Commits](spatialaudio/nbsphinx@0.9.3...0.9.5)

Updates `dunamai` from 1.19.2 to 1.22.0
- [Release notes](https://github.com/mtkennerly/dunamai/releases)
- [Changelog](https://github.com/mtkennerly/dunamai/blob/master/CHANGELOG.md)
- [Commits](mtkennerly/dunamai@v1.19.2...v1.22.0)

---
updated-dependencies:
- dependency-name: scikit-learn
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-packages
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: fire
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: cytominer-database
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-packages
- dependency-name: pytest
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: commitizen
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: ruff
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: mypy
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: mkdocs
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: sphinx-autoapi
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: ipython
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: nbsphinx
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python-packages
- dependency-name: dunamai
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
...

Signed-off-by: dependabot[bot] <[email protected]>

* revert to cytominer-database 3.4

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: d33bs <[email protected]>