Merge pull request #74 from haddocking/link-fix

Fix links

Author: sverhoeven

CONTRIBUTING.md

@@ -39,7 +39,7 @@ The sections below outline the steps in each case.
 1. lint your code with `uvx ruff check` (use `uvx ruff check --fix` to fix issues automatically);
 1. type check your code with `uv run pyrefly check src tests`;
 1. prevent code duplication, detect with `npx jscpd src`;
-1. update or expand the documentation (see [Contributing with documentation](#contributing-with-documentation) section below);
+1. update or expand the documentation (see [Contributing to documentation](#contributing-to-documentation) section below);
 1. [push](http://rogerdudler.github.io/git-guide/) your feature branch to (your fork of) the protein-quest repository on GitHub;
 1. create the pull request, e.g. following the instructions [here](https://help.github.com/articles/creating-a-pull-request/).
 

README.md

@@ -77,7 +77,7 @@ pip install git+https://github.com/haddocking/protein-quest.git
 
 The main entry point is the `protein-quest` command line tool which has multiple subcommands to perform actions.
 
-To use programmaticly, see the [Jupyter notebooks](https://www.bonvinlab.org/protein-quest/notebooks) and [API documentation](https://www.bonvinlab.org/protein-quest/autoapi/summary/).
+To use programmaticly, see the [Jupyter notebooks](https://www.bonvinlab.org/protein-quest/notebooks) and [API documentation](https://www.bonvinlab.org/protein-quest/autoapi/protein_quest/).
 
 While downloading or copying files it uses a global cache (located at `~/.cache/protein-quest`) and hardlinks to save disk space and improve speed.
 This behavior can be customized with the `--no-cache`, `--cache-dir`, and `--copy-method` command line arguments.
@@ -275,7 +275,7 @@ The mcp server contains an prompt template to search/retrieve/filter candidate s
 
 ## Shell autocompletion
 
-The `protein-quest` command line tool supports shell autocompletion using [shtab](https://shtab.readthedocs.io/).
+The `protein-quest` command line tool supports shell autocompletion using [shtab](https://docs.iterative.ai/shtab).
 
 Initialize for bash shell with:
 

src/protein_quest/alphafold/fetch.py

@@ -114,7 +114,6 @@ def relative_to(self, session_dir: Path) -> "AlphaFoldEntry":
         """Convert paths in an AlphaFoldEntry to be relative to the session directory.
 
         Args:
-            entry: An AlphaFoldEntry instance with absolute paths.
             session_dir: The session directory to which the paths should be made relative.
 
         Returns: