Streamline Dockerfile, remove unused deps

* Dockerfile: Use non-root user, buildx cache, setup for readonly
   container, remove unused apt deps.
   For now don't install pip package and keep development flask server
   as this will be replaced in the future (fastapi). Then a proper
   webserver (e.g. nginx) should be used and the pip package can be
   created and deployed just to the run-stage (with the webserver).
 * docker-compose: Set to readonly (anonymous volumes declared in
   Dockerfile should maintain all writable data).
   Mount config.py for easier development. Should be replaced by
   environment support for all config file variables.
 * Remove unused runtime dependencies: mariadb, joblib, pytest,
   pytest-cov.
 * Move pytest-cov to dev dependencies.
 * Add output_dir to config.py.
 * Fix visualization_results.pdf endpoint.
 * Update docs.

CONTRIBUTING.md

@@ -24,7 +24,7 @@ To make collaboration easier, we require pull requests to pass code style and un
 Our code style checks use [`pre-commit`](https://pre-commit.com).
 
 ```bash
-pip install -r requirements.txt
+pip install -r requirements-dev.txt
 ```
 
 To run formatting automatically before every commit:
@@ -36,7 +36,7 @@ pre-commit install
 Or run them manually:
 
 ```bash
-pre-commit --all
+pre-commit run --all-files
 ```
 
 ### Tests