Update ruff configuration

[sjvrijn]

Description

Updated pre-commit script to use new explicit ruff check . syntax and ruff section in pyproject.toml to put most settings under tool.ruff.lint as instructed by deprecation warnings

[!NOTE] Note: based on #374, so marked as draft until that one is merged

• [x] I have read the contribution guidelines
• [x] This update is in line with what is recommended in the Python chapter of the Guide

Related issues

• closes #378

Instructions to review the pull request

$ cookiecutter -c 378-ruff-config-update https://github.com/NLeSC/python-template
# Fill with python-template-test info... or just press 'enter' 12 times
$ cd python-template-test
$ git init
$ git config --local core.hooksPath .githooks  # enable pre-commit git hook
$ git add .
$ git commit -m "initial commit"
Script .githooks/pre-commit triggered ...
Starting ruff analysis...
All checks passed!
Pre-commit checks completed successfully.
...
<regular commit summary output>