Update agent instructions to prefer prek and uv run

.github/copilot-instructions.md

@@ -8,17 +8,30 @@ be deployed at https://microsoft.github.io/Qcodes/.
 
 The documentation includes Contributor's guide, so please follow that closely.
 
-Before committing anything, run pre-commit hooks with ```pre-commit run --all```
-and make sure they pass, and fix anything that is failing. The pre-commit hooks will ensure
-correct formatting of the code and linting as well. The pre-commit hooks are automatically installed
-so there is no need to manually install them.
+If the user manages the Python environment with ``uv``, always run commands that need that
+environment (``pytest``, ``pyright``, ``python`` etc.) via ``uv run``. Both ``pytest`` and
+``pyright`` need the test dependencies, so always run them with ``--extra test``, e.g.
+``uv run --extra test pytest tests`` and ``uv run --extra test pyright``. Without it ``uv run``
+only ensures that the core dependencies are installed, so the test dependencies may be missing.
+On Windows, where ``pyright`` is typically installed as an npm shim, use
+``uv run --extra test pyright.cmd``.
+Do not activate the virtual environment, call executables inside it directly, or point tools at
+an interpreter with options such as ``--pythonpath``; let ``uv run`` select the environment.
+
+Before committing anything, run pre-commit hooks and make sure they pass, and fix anything that
+is failing. If ``prek`` is available on the ``PATH``, use it via ``prek run --all-files``; otherwise
+use ``pre-commit run --all``. The hooks will ensure correct formatting of the code and linting as
+well. The hooks are automatically installed so there is no need to manually install them.
 
 QCoDeS is a typed package, hence all new code should include clear and correct type annotations.
 
 We use ``pyright`` to statically check the correctness of the code with type annotations.
-Run it via ``pyright``. The code that should be typecheked is configured in ``pyproject.toml``.
+Run it via ``pyright`` (or ``uv run --extra test pyright`` / ``uv run --extra test pyright.cmd``
+as described above).
+The code that should be typechecked is configured in ``pyproject.toml``.
 
-For running tests, we use ``pytest``. They can be run with ``pytest tests``.
+For running tests, we use ``pytest``. They can be run with ``pytest tests``
+(or ``uv run --extra test pytest tests`` as described above).
 See pytest markers for additional options of running tests.
 
 We use Dependabot from GitHub to keep our dependencies up to date, we use ``requirements.txt``