Add uv run hint to the uvx guide (#6454)

docs/guides/tools.md

@@ -41,6 +41,12 @@ $ uvx pycowsay hello from uv
 
 Tools are installed into temporary, isolated environments when using `uvx`.
 
+!!! note
+
+    If you are running a tool in a [_project_](../concepts/projects.md) and the tool requires that your project is installed,
+    e.g., when using `pytest` or `mypy`, you'll want to use [`uv run`](./projects.md#running-commands) instead of `uvx`.
+    Otherwise, the tool will be run in a virtual environment that is isolated from your project.
+
 ## Commands with different package names
 
 When `uvx ruff` is invoked, uv installs the `ruff` package which provides the `ruff` command.