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doc: add documentation for the lineage_definitions format #652

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merged 1 commit into from
Nov 27, 2024

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Taepper
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@Taepper Taepper commented Nov 27, 2024

Summary

Add documentation for the lineage definitions file, which is required for the specification of monophyletic sublineage queries.

PR Checklist

  • All necessary documentation has been adapted or there is an issue to do so.
  • The implemented feature is covered by an appropriate test.

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There is no change in the changelog. This PR will not produce a new releasable version.

@Taepper Taepper force-pushed the lineage-defininitions-doc branch 2 times, most recently from f00f6bb to 8b96072 Compare November 27, 2024 08:04
@fengelniederhammer fengelniederhammer added the documentation Improvements or additions to documentation label Nov 27, 2024
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Linking GenSpectrum/LAPIS#978 for reference.

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What's the scope of this? This is a very formal description. For a quick "let's pin down the schema", this is good. But it's not something that maintainers would understand, because it's not comprehensive enough (IMO). What does it mean to define those lineage? What consequences does it have on the data at runtime? How can users query it?

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Taepper commented Nov 27, 2024

I wanted something that is at least one step above "ah, I found an example in the codebase" which is what happened now for Loculus ^^

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I agree, this is definitely better than nothing. I don't want to block here, we can improve it later.

@Taepper Taepper force-pushed the lineage-defininitions-doc branch from 8b96072 to 0983f88 Compare November 27, 2024 08:53
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Taepper commented Nov 27, 2024

Ok, fixed a typo in the commit message and will merge afterward

@Taepper Taepper changed the title doc: add documentation for the lienage_definitions format doc: add documentation for the lineage_definitions format Nov 27, 2024
@Taepper Taepper merged commit bbfa8e6 into main Nov 27, 2024
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@Taepper Taepper deleted the lineage-defininitions-doc branch November 27, 2024 09:02
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2 participants