Bump the poetry-dependencies group with 20 updates (#38)

Bumps the poetry-dependencies group with 20 updates:

| Package | From | To |
| --- | --- | --- |
| [numpy](https://github.com/numpy/numpy) | `2.2.1` | `2.2.2` |
| [scipy](https://github.com/scipy/scipy) | `1.14.1` | `1.15.1` |
| [biopython](https://github.com/biopython/biopython) | `1.84` | `1.85` |
| [pygments](https://github.com/pygments/pygments) | `2.18.0` | `2.19.1` |
| [black](https://github.com/psf/black) | `24.10.0` | `25.1.0` |
| [pre-commit](https://github.com/pre-commit/pre-commit) | `4.0.1` | `4.1.0` |
| [ruff](https://github.com/astral-sh/ruff) | `0.8.4` | `0.9.4` |
| [sphinx-autodoc-typehints](https://github.com/tox-dev/sphinx-autodoc-typehints) | `2.5.0` | `3.0.1` |
| [anyio](https://github.com/agronholm/anyio) | `4.7.0` | `4.8.0` |
| [certifi](https://github.com/certifi/python-certifi) | `2024.12.14` | `2025.1.31` |
| [executing](https://github.com/alexmojaki/executing) | `2.1.0` | `2.2.0` |
| [filelock](https://github.com/tox-dev/py-filelock) | `3.16.1` | `3.17.0` |
| [identify](https://github.com/pre-commit/identify) | `2.6.4` | `2.6.6` |
| [ipython](https://github.com/ipython/ipython) | `8.31.0` | `8.32.0` |
| [prompt-toolkit](https://github.com/prompt-toolkit/python-prompt-toolkit) | `3.0.48` | `3.0.50` |
| ruamel-yaml | `0.18.7` | `0.18.10` |
| [starlette](https://github.com/encode/starlette) | `0.45.1` | `0.45.3` |
| [virtualenv](https://github.com/pypa/virtualenv) | `20.28.0` | `20.29.1` |
| [watchfiles](https://github.com/samuelcolvin/watchfiles) | `1.0.3` | `1.0.4` |
| [websockets](https://github.com/python-websockets/websockets) | `14.1` | `14.2` |


Updates `numpy` from 2.2.1 to 2.2.2
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v2.2.1...v2.2.2)

Updates `scipy` from 1.14.1 to 1.15.1
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.14.1...v1.15.1)

Updates `biopython` from 1.84 to 1.85
- [Changelog](https://github.com/biopython/biopython/blob/master/NEWS.rst)
- [Commits](https://github.com/biopython/biopython/commits)

Updates `pygments` from 2.18.0 to 2.19.1
- [Release notes](https://github.com/pygments/pygments/releases)
- [Changelog](https://github.com/pygments/pygments/blob/master/CHANGES)
- [Commits](pygments/pygments@2.18.0...2.19.1)

Updates `black` from 24.10.0 to 25.1.0
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](psf/black@24.10.0...25.1.0)

Updates `pre-commit` from 4.0.1 to 4.1.0
- [Release notes](https://github.com/pre-commit/pre-commit/releases)
- [Changelog](https://github.com/pre-commit/pre-commit/blob/main/CHANGELOG.md)
- [Commits](pre-commit/pre-commit@v4.0.1...v4.1.0)

Updates `ruff` from 0.8.4 to 0.9.4
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.8.4...0.9.4)

Updates `sphinx-autodoc-typehints` from 2.5.0 to 3.0.1
- [Release notes](https://github.com/tox-dev/sphinx-autodoc-typehints/releases)
- [Commits](tox-dev/sphinx-autodoc-typehints@2.5.0...3.0.1)

Updates `anyio` from 4.7.0 to 4.8.0
- [Release notes](https://github.com/agronholm/anyio/releases)
- [Changelog](https://github.com/agronholm/anyio/blob/master/docs/versionhistory.rst)
- [Commits](agronholm/anyio@4.7.0...4.8.0)

Updates `certifi` from 2024.12.14 to 2025.1.31
- [Commits](certifi/python-certifi@2024.12.14...2025.01.31)

Updates `executing` from 2.1.0 to 2.2.0
- [Release notes](https://github.com/alexmojaki/executing/releases)
- [Commits](alexmojaki/executing@v2.1.0...v2.2.0)

Updates `filelock` from 3.16.1 to 3.17.0
- [Release notes](https://github.com/tox-dev/py-filelock/releases)
- [Changelog](https://github.com/tox-dev/filelock/blob/main/docs/changelog.rst)
- [Commits](tox-dev/filelock@3.16.1...3.17.0)

Updates `identify` from 2.6.4 to 2.6.6
- [Commits](pre-commit/identify@v2.6.4...v2.6.6)

Updates `ipython` from 8.31.0 to 8.32.0
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](ipython/ipython@8.31.0...8.32.0)

Updates `prompt-toolkit` from 3.0.48 to 3.0.50
- [Release notes](https://github.com/prompt-toolkit/python-prompt-toolkit/releases)
- [Changelog](https://github.com/prompt-toolkit/python-prompt-toolkit/blob/master/CHANGELOG)
- [Commits](prompt-toolkit/python-prompt-toolkit@3.0.48...3.0.50)

Updates `ruamel-yaml` from 0.18.7 to 0.18.10

Updates `starlette` from 0.45.1 to 0.45.3
- [Release notes](https://github.com/encode/starlette/releases)
- [Changelog](https://github.com/encode/starlette/blob/master/docs/release-notes.md)
- [Commits](encode/starlette@0.45.1...0.45.3)

Updates `virtualenv` from 20.28.0 to 20.29.1
- [Release notes](https://github.com/pypa/virtualenv/releases)
- [Changelog](https://github.com/pypa/virtualenv/blob/main/docs/changelog.rst)
- [Commits](pypa/virtualenv@20.28.0...20.29.1)

Updates `watchfiles` from 1.0.3 to 1.0.4
- [Release notes](https://github.com/samuelcolvin/watchfiles/releases)
- [Commits](samuelcolvin/watchfiles@v1.0.3...v1.0.4)

Updates `websockets` from 14.1 to 14.2
- [Release notes](https://github.com/python-websockets/websockets/releases)
- [Commits](python-websockets/websockets@14.1...14.2)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: poetry-dependencies
- dependency-name: scipy
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
- dependency-name: biopython
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
- dependency-name: pygments
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
- dependency-name: black
  dependency-type: direct:development
  update-type: version-update:semver-major
  dependency-group: poetry-dependencies
- dependency-name: pre-commit
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
- dependency-name: ruff
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
- dependency-name: sphinx-autodoc-typehints
  dependency-type: direct:development
  update-type: version-update:semver-major
  dependency-group: poetry-dependencies
- dependency-name: anyio
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
- dependency-name: certifi
  dependency-type: indirect
  update-type: version-update:semver-major
  dependency-group: poetry-dependencies
- dependency-name: executing
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
- dependency-name: filelock
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
- dependency-name: identify
  dependency-type: indirect
  update-type: version-update:semver-patch
  dependency-group: poetry-dependencies
- dependency-name: ipython
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
- dependency-name: prompt-toolkit
  dependency-type: indirect
  update-type: version-update:semver-patch
  dependency-group: poetry-dependencies
- dependency-name: ruamel-yaml
  dependency-type: indirect
  update-type: version-update:semver-patch
  dependency-group: poetry-dependencies
- dependency-name: starlette
  dependency-type: indirect
  update-type: version-update:semver-patch
  dependency-group: poetry-dependencies
- dependency-name: virtualenv
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
- dependency-name: watchfiles
  dependency-type: indirect
  update-type: version-update:semver-patch
  dependency-group: poetry-dependencies
- dependency-name: websockets
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
...

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