Update instance repo from cookiecutter template

pyproject.toml

@@ -64,6 +64,9 @@ addopts = [
 [tool.ruff]
 src = ["src"]
 line-length = 120
+extend-include = ["*.ipynb"]
+
+[tool.ruff.lint]
 select = [
     "F",  # Errors detected by Pyflakes
     "E",  # Error detected by Pycodestyle
@@ -104,15 +107,14 @@ ignore = [
     # We want docstrings to start immediately after the opening triple quote
     "D213",
 ]
-extend-include = ["*.ipynb"]
 
 [tool.ruff.format]
 docstring-code-format = true
 
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "docs/*" = ["I"]
 "tests/*" = ["D"]
 "*/__init__.py" = ["F401"]