chore: 📦 Update dependencies (#456)

This PR updates the lockfile to the latest versions of the dependencies.
Please review the changes and merge when ready.

---------

Co-authored-by: Alessandro Angioi <alessandro.angioi@simulation.science>

Author: PasteurBot

inject_runtime_pyproject.py

@@ -12,7 +12,7 @@
 
 BASE_OPTIONAL_DEPS = {
     "docs": [
-        "sphinx",
+        "sphinx<9",  # TODO: Remove when sphinx-click supports sphinx 9 (https://github.com/click-contrib/sphinx-click/issues/159)
         "sphinx_autodoc_typehints",
         "furo",
         "myst-nb",