Switch to GitHub actions for CI #316
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Definitely worth looking into! It shouldn't be too much trouble to yank some stuff from the EMPress GH Actions pipeline for use with Qurro. Although I'm not sure this is urgent, at least right now -- development on Qurro has slowed down over the past year, so I don't think we're in danger of exceeding the monthly time limit on CI from Travis. Unless people start submitting zillions of PRs here all of a sudden ;) |
fedarko
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Yeah definitely not a pressing issue. Just thought of it since I'm going to start working on the QIIME 2 plugin for BIRDMAn and remembered that interval support was something we wanted to add in Qurro (#222) |
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That's super exciting! Yeah, in that case it might be worth taking some time to port the CI over to GitHub actions. Def let me know when you get to the point of hooking BIRDMAn up to Qurro -- I think it would probably take a day or two to get things set up so that Qurro could display error bars; I'm happy to help out with that push :) |
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fedarko
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…QIIME 2 (#322) * DEP: Update setup.py re: python and pandas #315 * DEV: port CI from Travis to GH Actions: close #316 * 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) * DEP: pin min biom vsn and add some comments * DEP: Fix biom_table_to_sparse_df for pandas >= 1 See #258 and #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 * DEP: remove some warnings, docs, fix a test re: pd * TST: Fix the python tests!!! #258 The problem was using .loc[] on these sparse dataframes. whoops * STY: tiny style fixes * DEP: knock out some pandas warnings * DEP: np.matrix() -> np.array() in qarcoal tests since apparently it's deprecated, or about to be deprecated, idk * DEP/STY: Fix more warnings; remove unused import most of these warnings were just pd.DataFrame.append() being deprecated and replaced with pd.concat() * 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 * DOC: update readme re: min Q2 vsn * TST: matrix of qiime 2 versions nice! * TST: more detailed comment about Q2 vsn matrix * DOC: remove the "Sparse" from "SparseDataFrame" * REL: version kick * 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.) * TST: attempt to get standalone tests working * TST: attempt to fix pytest q2 exclusion * DEP: ok py 3.10 is a no go * STY: fix formatting * DOC: Rerun 4 / 6 example notebooks Songbird and ALDEx2 ones will cause problems * DOC: tidy/update readme refs * DOC: update jake fish dataset ref on website * DOC: Fix songbird notebook!, standardize output rm * BLD: rm (now-)unused comments from q2 ci * DOC: fix transcriptomics ntbk :) * REL: update changelog * REL: update changelog * 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 * 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 * DOC: songbird compatibility deets * DEV/DOC: update dev docs re: 2022 the apocalypse came and all i got was this pull request * REL: update changelog about updating contributing about about about about aboot * REL: minor chglog tidying
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The new Travis pricing rules make switching to GH Actions a better alternative. See this issue from EMPress.
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