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Update Qurro to support pandas v1 and up, and thus newer versions of QIIME 2 #322

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merged 36 commits into from
Oct 20, 2022

Commits on Jul 5, 2022

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  3. TST: For now, omit "make notebooks" from CI

    Maybe we can make another GitHub Actions for these later; but
    Songbird is causing tensorflow nonsense to pop up, and this is not
    the sort of thing I think we should spend time fixing (esp with
    the advent of birdman)
    fedarko committed Jul 5, 2022
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  5. DEP: Fix biom_table_to_sparse_df for pandas >= 1

    See biocore#258 and biocore#315. not confident this is done yet (and if nothing
    else the rest of the code gleefully refers to "SparseDataFrame"
    because 2019 marcus was a schmuck), but this at least fixes a fair
    amount of failing tests
    fedarko committed Jul 5, 2022
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  7. TST: Fix the python tests!!! biocore#258

    The problem was using .loc[] on these sparse dataframes. whoops
    fedarko committed Jul 5, 2022
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  8. STY: tiny style fixes

    fedarko committed Jul 5, 2022
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  10. DEP: np.matrix() -> np.array() in qarcoal tests

    since apparently it's deprecated, or about to be deprecated, idk
    fedarko committed Jul 5, 2022
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  11. DEP/STY: Fix more warnings; remove unused import

    most of these warnings were just pd.DataFrame.append() being
    deprecated and replaced with pd.concat()
    fedarko committed Jul 5, 2022
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  12. DOC: one of the demos' JS data slightly changed

    looks like it's a tiny floating-point thing -- probably an artifact
    of working here on a new operating system, on a new python version,
    a new pandas version, a new biom version, etc. shouldn't make a
    noticeable difference
    fedarko committed Jul 5, 2022
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  14. TST: matrix of qiime 2 versions

    nice!
    fedarko committed Jul 5, 2022
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  17. REL: version kick

    fedarko committed Jul 5, 2022
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  18. TST: Add standalone CI

    IIRC something about how our specific altair version works makes it
    incompatible with python 3.10. let's test that here -- if needed,
    we can update the README to disallow python versions >= 3.10. (And
    then we can look into removing the altair pin when absolutely needed.)
    fedarko committed Jul 5, 2022
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  21. DEP: ok py 3.10 is a no go

    fedarko committed Jul 5, 2022
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  22. STY: fix formatting

    fedarko committed Jul 5, 2022
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  23. DOC: Rerun 4 / 6 example notebooks

    Songbird and ALDEx2 ones will cause problems
    fedarko committed Jul 5, 2022
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Commits on Jul 6, 2022

  1. DOC: tidy/update readme refs

    fedarko committed Jul 6, 2022
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  6. REL: update changelog

    fedarko committed Jul 6, 2022
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  7. REL: update changelog

    fedarko committed Jul 6, 2022
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  8. TST: see if we can finagle q2 2020.6 / 2020.8?

    since i thiiiink these versions mighta worked with the pandas >= 1
    syntax
    
    that being said, i don't think it makes sense to devote time/energy
    to officially supporting them; just wanna check
    fedarko committed Jul 6, 2022
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  9. TST: remove Q2 2020.6 / 2020.8 in CI

    Looks like the tests themselves pass for these versions, but the
    style-checking with black fails due to incompatibility with click.
    
    yeah this is enough for me to not bother supporting these versions
    imo
    fedarko committed Jul 6, 2022
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  11. DEV/DOC: update dev docs re: 2022

    the apocalypse came and all i got was this pull request
    fedarko committed Jul 6, 2022
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  12. REL: update changelog about updating contributing

    about about about about aboot
    fedarko committed Jul 6, 2022
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  13. REL: minor chglog tidying

    fedarko committed Jul 6, 2022
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