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export multiple trees #1450

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Commits on May 6, 2024

  1. [export] enforce tree naming standards 

    Checking for duplicated node names and missing node names is in line
with the schema. Previously some calls to `export v2` would be ok with
missing node names (e.g. see the updated tests in `minify-output.t`) but
any usage with metadata would result in an uncaught error.
    @jameshadfield
    jameshadfield committed May 6, 2024
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  2. [export] allow multiple trees 

    Multiple trees ("subtrees") have been available in Auspice since late
2021¹ and part of the associated schema since early 2022². Despite this
there was no way to produce such datasets within Augur itself, and
despite the schema changes the associated `augur validate` command was
never updated to allow them.

This commit adds multi-tree inputs to `augur export v2` as well as
allowing them to validate with our associated validation commands.

¹ <nextstrain/auspice#1442>
² <#851>
    @jameshadfield
    jameshadfield committed May 6, 2024
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  3. [export] refactor to always use a list of trees 

    Always use a list of trees, even if it's a one-item list. This
simplifies internal logic by avoiding the need to check data type on
every reference. Requested via code review¹

¹ <#1450 (comment)>
    @jameshadfield
    jameshadfield committed May 6, 2024
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