Implicit multiple trajectories

[Jacob-Stevens-Haas]

For your consideration, here's a PR that implements #353.

tl;dr: IMO the multiple_trajectories argument is unneccessary and its removal simplifies calling signatures. SINDy.fit() knows users want multiple trajectories when they pass a list of arrays - the same way many numpy functions have implicit behavior when passed a list of arrays instead of a single array. OTOH, there exists a niche case where someone calls fit() with x as a list instead of an array and t as a float. Previously, this would give an error, while in this PR, it would be allowed, similar to how submitting transposed data is allowed but doesn't give people what they think. If people desire, I can add guard code around specifically this case, but my feeling is that the docstring is clear and the edge case may not exist in the wild.

[Jacob-Stevens-Haas]

So this passes in 3.10, but fails <3.10 because isinstance didn't used to work for subscripted generics... working on a fix.

[codecov]

Codecov Report

Patch coverage: 100.00% and project coverage change: +0.10% 🎉

Comparison is base (044b4f5) 93.70% compared to head (fe3e4ad) 93.81%.
Report is 3 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #376      +/-   ##
==========================================
+ Coverage   93.70%   93.81%   +0.10%     
==========================================
  Files          37       37              
  Lines        3589     3604      +15     
==========================================
+ Hits         3363     3381      +18     
+ Misses        226      223       -3     

Files Changed	Coverage Δ
pysindy/pysindy.py	97.17% <100.00%> (+0.14%)	⬆️
pysindy/utils/base.py	85.62% <100.00%> (+1.89%)	⬆️

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[Jacob-Stevens-Haas]

This counts as green CI, I believe. Similar situation as before - deletion PR with 100% of diff covered, but because covered lines were deleted, overall coverage drops.

[znicolaou]

I'm good with this change! Only request: run each of the example notebooks to verify that the edge case doesn't need to be eliminated in the notebooks.

[Jacob-Stevens-Haas]

Thanks @znicolaou! I searched through all the notebooks, and anything that used discrete_time=True made sure to cast each trajectory as a numpy array before fit(). But since master is tracking a 2.0 release, most of the notebooks fail for other breaks in backwards compatibility during the last few PRs.

My short fix for the notebooks (later; as we get closer to 2.0) will be to add an assert pysindy.__version__ < 2 to the first cell of any notebook that isn't in a fast-testable format. Right now that's everything other than 1, 2, and 5. Long term, we should talk about how to revamp examples/documentation, e.g. whether to pin examples to specific versions of pysindy. I feel like it's reasonable, if API reference is correct, to expect a user to be able to update any code based upon a research example notebook pinned to an old version. e.g. ensembling.