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

[fedarko]

• Port CI from Travis to GitHub Actions (close Switch to GitHub actions for CI #316)

  • Made use of the nice matrix functionality in GitHub Actions to automatically test on multiple QIIME 2 versions.
  • Currently, we just test on the oldest and newest QIIME 2 versions that Qurro supports (2020.11 and whatever the latest is). (The reason 2020.11 is the oldest Q2 version we support is because it's the first that switched over to pandas >= 1.)
  • Added a standalone CI, analogous to EMPress' standalone CI.

• Updated the code to not use pd.SparseDataFrame, and instead use pd.DataFrame with sparse arrays (close Support pandas v1: Switch from SparseDataFrame to "regular ... DataFrame with sparse values" #258, close Qurro will break on newer (>= 2020.11) versions of QIIME 2 #315)

  • This required much less work than it sounds like, because biom.Table.to_dataframe() does all the heavy lifting. Previously, Qurro was actively avoiding using that function due to a bug with it ([python] to_dataframe does not produce sparse data frames biom-format#808), but -- now that that bug is fixed in all biom versions that Qurro accepts -- we can just delegate to it.

• Updated the code to remove various sources of warnings. A lot of things have become deprecated in the past few years (e.g. pd.DataFrame.append(), using a set as an indexer in pandas, np.matrix, ...)

• Updated the documentation regarding the minimum Q2 version stuff

This PR is almost ready to go -- the main things I need to fix are

• rerunning all of the example notebooks now that there aren't five million warnings being created from Support pandas v1: Switch from SparseDataFrame to "regular ... DataFrame with sparse values" #258
  • as an extra difficulty spike, some of the dependencies of these notebooks are now incompatible with the sort of conda environments we set up (e.g. Songbird explicitly requires a pandas version < 1). There are various ways to get around this, ranging from "convert the notebooks to markdowns and call it a day", "split into separate notebooks", etc; let's see what's easiest.
• updating the changelog

[codecov-commenter]

Codecov Report

Merging #322 (994cc18) into master (005cc44) will decrease coverage by 9.56%.
The diff coverage is 75.00%.

@@            Coverage Diff             @@
##           master     #322      +/-   ##
==========================================
- Coverage   95.09%   85.53%   -9.57%     
==========================================
  Files          19       19              
  Lines        1408     1417       +9     
  Branches      234      237       +3     
==========================================
- Hits         1339     1212     -127     
- Misses         57      193     +136     
  Partials       12       12              

Impacted Files	Coverage Δ
qurro/_json_utils.py	92.38% <ø> (ø)
qurro/_metadata_utils.py	87.87% <ø> (-6.07%)	⬇️
qurro/generate.py	97.56% <ø> (ø)
qurro/q2/_visualizers.py	0.00% <ø> (-100.00%)	⬇️
qurro/qarcoal.py	0.00% <0.00%> (-100.00%)	⬇️
qurro/scripts/_plot.py	88.23% <ø> (ø)
qurro/__init__.py	100.00% <100.00%> (ø)
qurro/_df_utils.py	97.33% <100.00%> (-0.06%)	⬇️
qurro/_rank_utils.py	100.00% <100.00%> (ø)
qurro/support_files/js/display.js	95.86% <100.00%> (+0.08%)	⬆️
... and 8 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 2509145...994cc18. Read the comment docs.

[gibsramen]

• as an extra difficulty spike, some of the dependencies of these notebooks are now incompatible with the sort of conda environments we set up (e.g. Songbird explicitly requires a pandas version < 1). There are various ways to get around this, ranging from "convert the notebooks to markdowns and call it a day", "split into separate notebooks", etc; let's see what's easiest.

Honestly I think we should just not run the notebooks and keep them static. Dependencies issues are going to accumulate and I don't think we should be expected to maintain them continually specifically for notebooks. Maybe just add a note that dependencies may have changed since creation. (Willing to change my mind on this, though.)

[fedarko]

Honestly I think we should just not run the notebooks and keep them static. Dependencies issues are going to accumulate and I don't think we should be expected to maintain them continually specifically for notebooks. Maybe just add a note that dependencies may have changed since creation. (Willing to change my mind on this, though.)

That's fair -- this is definitely the more sustainable way to handle this :) That being said, I figure things are pretty stable for the time being: after looking into things, the bulk of the problems wound up coming from Songbird now being incompatible with Qurro's environments.

In my opinion, supporting the combo of Songbird + Qurro is important, so I took some time and updated the "Red Sea" notebook to explain how to run Songbird and Qurro in separate conda environments. That fixed most of the problems (the other main thing was updating the ALDEx2 notebook, which wasn't too bad); the notebooks are now all up-to-date (and, as a nice bonus, now the users don't see all of those pandas warnings about SparseDataFrame being deprecated...) However, if things break horribly in a month, ... then I'll probably just add a note, like you suggest.

This PR should now be ready for review / merging.