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@gsfk gsfk commented Nov 11, 2025

I am a longtime phenopackets user and I lean heavily on the documentation page, so thanks for that. In honour of "phenopackets docs fest" I offer some documentation fixes that I hope will eliminate a lot of confusion... at least on my part.

The documentation has entries for several fields that are not part of any version of the specification. It seems like these fields were in development for phenopackets version 2, but then never adopted, or were adopted under a different name, but then the documentation was not updated accordingly.

This PR removes docs for the following fields, none of which exist in the schema:

  • ApiVersion, removed from the spec here
  • Exposure, removed here
  • Interval, replaced by TimeInterval here
  • Pharmaceutical Treatment, replaced here
  • StopReason, removed here

Some but not all of these were orphaned in the sense that they could not be found by clicking through the readthedocs page, but all are returned by the search feature on the same page. So if you search for "exposure" you will be led to a page that falsely claims that Exposure is a top-level phenopackets field. I believe this has caused confusion among phenopackets users before.

I also removed this orphaned page, again discoverable only through search, that describes version 2 as in progress and contained the only references to these erroneous fields (except for StopReason, which is still listed as a building block).

For fields that were renamed or replaced, the correct documentation exists already under the appropriate name.

Resolves issue #395. Cheers!

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