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Update Qurro to support pandas v1 and up, and thus newer versions of QIIME 2 #322
Commits on Jul 5, 2022
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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)
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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
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TST: Fix the python tests!!! biocore#258
The problem was using .loc[] on these sparse dataframes. whoops
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DEP: np.matrix() -> np.array() in qarcoal tests
since apparently it's deprecated, or about to be deprecated, idk
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DEP/STY: Fix more warnings; remove unused import
most of these warnings were just pd.DataFrame.append() being deprecated and replaced with pd.concat()
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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
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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.)
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DOC: Rerun 4 / 6 example notebooks
Songbird and ALDEx2 ones will cause problems
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Commits on Jul 6, 2022
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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
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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
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DEV/DOC: update dev docs re: 2022
the apocalypse came and all i got was this pull request
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REL: update changelog about updating contributing
about about about about aboot
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