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The error in tskit-dev/tskit-site#182 is caused due to some bugs in Jupyter Book to process toctree with Sphinx autosummary (jupyter-book/jupyter-book#1145).
I have modified the API documentation like msprime's API documentation (https://github.com/tskit-dev/msprime/blob/main/docs/api.md), and I believe that there will be no errors when we build the documentation this time.
@jeromekelleher Would it be possible for you to approve this pull request and reconduct the pull request in tskit-dev/tskit-site#182?