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Bsweger/more state permutations/37 #45

Merged
merged 8 commits into from
Oct 28, 2024
Merged

Bsweger/more state permutations/37 #45

merged 8 commits into from
Oct 28, 2024

Commits on Oct 28, 2024

  1. Fix a rookie mistake

    @bsweger
    bsweger committed Oct 28, 2024
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  2. Add paramater to specify state format in metadata "location" column 

    This is a potential breaking change to anyone who was relying on
full state name in the location field of sequence metadata
datasets. The default is now the two letter state abbreviation,
which is more commonly used in hub tasks.json files.
    @bsweger
    bsweger committed Oct 28, 2024
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  3. Rename typing

    @bsweger
    bsweger committed Oct 28, 2024
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  4. Update documentation

    @bsweger
    bsweger committed Oct 28, 2024
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  5. Move sequence file and rename filter function 

    Documenting the filter_covid_genome_metadata function made it
clear that its name should better align with the CladeTime
vernacular ('sequence metadata'). Additionally, it makes more
sense to move sequence.py out of the utility folder, since
sequence-related functions are integral to the package.

util/sequence.py remains in the code base for now, so we can
import the filtering function with its old name for backward
compatibility.
    @bsweger
    bsweger committed Oct 28, 2024
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  6. fix up some merge conflicts

    @bsweger
    bsweger committed Oct 28, 2024
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  7. Update filter_sequence_metadata docstring 

    This function can also accept and return a polars DataFrame
(in addition to a LazyFrame)
    @bsweger
    bsweger committed Oct 28, 2024
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  8. Falsy fix

    @bsweger
    bsweger committed Oct 28, 2024
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