Hi @jonbrenas ,

I’ve scoped this PR to the minimal changes requested in #809, removing usage examples and exposing the phenotype methods in the API docs.

While working on this, I noticed some areas in the phenotype docstrings (e.g. type hints, consistency, edge-case notes) that could benefit from clarification and cleanup. If that sounds useful, I’d be happy to open a follow-up PR focused purely on improving documentation. Let me know what you think!

Thanks @mohamed-laarej. This is the perfect PR for all documentation tasks, feel free to make all the changes that you think would improve things.

Thanks @mohamed-laarej.

The way the documentation is generated, the description of the function and of its outputs ought to be before the function definition and look something like this :

            Run a H1X genome-wide scan to detect genome regions with
            shared selective sweeps between two cohorts.
        """,
        returns=dict(
            x="An array containing the window centre point genomic positions.",
            h1x="An array with H1X statistic values for each window.",
            contigs="An array with the contig for each window. The median is chosen for windows overlapping a change of contig.",
        )```

The parameters ought to be described in th `*_params.py` files. Does that make sense? Can you update your code to follow this standard?

Thanks @jonbrenas for the clarification! I’ll update the docstrings to use the @doc decorator and revise them to follow your feedback and the API documentation standards.

Looks like this just needs an update from the base branch and then a re-review.