Update docs regarding pre-commit and ruff. [ci skip]

Author: lohedges

doc/source/contributing/codestyle.rst

@@ -53,10 +53,10 @@ and now has a fully `PEP8-compliant <https://pep8.org>`__ API. We indent to
 move BioSimSpace towards using Python compliant API too, while preserving backwards
 compatibility.)
 
-We use `black <https://black.readthedocs.io/en/stable>`__ to autoformat our
-Python code. Please use this if you plan on submitting code. They are easy to
-configure and use via your IDE (or from the command-line) and help ensure a
-consistent code style and minimise diffs during pull requests.
+We use `ruff <https://docs.astral.sh/ruff>`__ to format and lint our Python
+code. This is run automatically via `pre-commit <https://pre-commit.com>`__
+hooks when you commit changes. See the :doc:`development` guide for setup
+instructions.
 
 Modules
 -------

doc/source/contributing/development.rst

@@ -185,18 +185,31 @@ Now create and switch to a feature branch. This should be prefixed with
    git checkout -b feature-process
 
 While working on your feature branch you won't want to continually re-install
-in order to make the changes active. To avoid this, you can either make use
-of ``PYTHONPATH``, e.g.
+in order to make the changes active. To avoid this, install the package in
+editable mode:
 
 .. code-block:: bash
 
-   PYTHONPATH=$HOME/Code/BioSimSpace/python python script.py
+   pip install -e .
 
-or use the ``develop`` argument when running the ``setup.py`` script, i.e.
+Pre-commit hooks
+----------------
+
+Pre-commit hooks are used to ensure consistent code formatting and linting.
+To set up pre-commit in your development environment:
+
+.. code-block:: bash
+
+   pixi shell -e dev
+   pre-commit install
+
+This will run `ruff <https://docs.astral.sh/ruff/>`__ formatting and linting
+checks automatically on each commit. To run the checks manually against all
+files:
 
 .. code-block:: bash
 
-   python setup.py develop
+   pre-commit run --all-files
 
 Testing
 -------