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Allow customization of input metadata delimiter #1196

Merged
merged 5 commits into from
Apr 12, 2023
Merged

Allow customization of input metadata delimiter #1196

merged 5 commits into from
Apr 12, 2023

Commits on Apr 12, 2023

  1. Allow customization of input metadata delimiter 

    Previously, there was hardcoded support for `,` and `\t`. Remove the hardcoding by:

1. Making valid delimiters a required parameter to `read_metadata()`.
2. In subcommands, adding a new flag `--metadata-valid-delimiters` with
   a default of the previously hardcoded delimiters, and passing that
   list into `read_metadata()`.
    @victorlin
    victorlin committed Apr 12, 2023
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  2. Update changelog for metadata delimiter changes

    @victorlin
    victorlin committed Apr 12, 2023
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  3. filter: Remove example ID columns from help text 

    These examples are already shown in the help text with the default
value.
    @victorlin
    victorlin committed Apr 12, 2023
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  4. Clarify single-value inference of some options 

    The previous wording of these option descriptions did not rule out using
multiple values at once. This change makes it clear that only one value
is inferred.
    @victorlin
    victorlin committed Apr 12, 2023
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  5. filter: Clarify behavior of --metadata-id-columns 

    Copy useful wording from the corresponding parameter description in
augur.io.metadata.read_metadata().
    @victorlin
    victorlin committed Apr 12, 2023
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