Merge pull request #64 from haddocking/clone-quest-58

Add instructions to clone protein-quest repo

Author: sverhoeven

CONTRIBUTING.md

@@ -31,6 +31,13 @@ The sections below outline the steps in each case.
 1. (**important**) announce your plan to the rest of the community *before you start working*. This announcement should be in the form of a (new) issue;
 1. (**important**) wait until some kind of consensus is reached about your idea being a good idea;
 1. if needed, fork the repository to your own Github profile and create your own feature branch off of the latest main commit. While working on your feature branch, make sure to stay up to date with the main branch by pulling in changes, possibly from the 'upstream' repository (follow the instructions [here](https://help.github.com/articles/configuring-a-remote-for-a-fork/) and [here](https://help.github.com/articles/syncing-a-fork/));
+1. clone the [protein-quest](https://github.com/haddocking/protein-quest) repository into the parent directory (one level up from protein-detective), since protein-detective depends on it during development:
+    ```shell
+    cd ..
+    git clone git@github.com:haddocking/protein-quest.git
+    cd protein-detective
+    ```
+    Since protein-quest is installed as a [source dependency](https://docs.astral.sh/uv/concepts/projects/dependencies/#dependency-sources), any changes you make to its code will be immediately available in protein-detective without needing to reinstall it.
 1. install [uv](https://docs.astral.sh/uv) to manage this packages development environment);
 1. Make sure `uv sync && . .venv/bin/activate && protein-detective --help` works;
 1. make sure the existing tests still work by running `uv run pytest`;

benchmark/stats.py

@@ -1,4 +1,5 @@
 """Script to print some statistics about the (partially) completed datasets."""
+
 # ruff: noqa: T201 this is a script
 from os import listdir
 from pathlib import Path