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filter: Remove attempt at extracting variables from --query #1278

Merged
merged 5 commits into from
Aug 14, 2023
Merged

filter: Remove attempt at extracting variables from --query #1278

merged 5 commits into from
Aug 14, 2023

Commits on Aug 12, 2023

  1. Add test showing existing behavior

    @victorlin
    victorlin committed Aug 12, 2023
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  2. filter: Remove attempt at extracting variables from --query 

    The attempt worked under limited testing, but introduced a bug that can
only be resolved with further complex Pandas query parsing. I don't
think that road is worth pursuing at the moment, so it's better to drop
the effort entirely.

This partially reverts commit 2ead5b3
and related changes.

I chose to keep the definition of PandasUndefinedVariableError at the
top-level¹ because it keeps external references next to each other, and
typing_extensions in the dependency list² because it is bound to be
useful at some point, and updating dependencies on Augur's Bioconda
recipe is a hassle.

¹ 602e3d5
² 2658659
    @victorlin
    victorlin committed Aug 12, 2023
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  3. Update changelog

    @victorlin
    victorlin committed Aug 12, 2023
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  4. cram: Add filter-query-and-exclude-ambiguous-dates-by test 

    Shows the interaction between the query and exclude-ambiguous-dates-by
options. This test currently does not work as intended and will be fixed
in the following commit.
    @joverlee521 @victorlin
    joverlee521 authored and victorlin committed Aug 12, 2023
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  5. Do type conversions on a copy of the metadata 

    This fixes the unexpected behavior described in the previous commit.
    @victorlin
    victorlin committed Aug 12, 2023
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