Update Starfish CI and dependencies

[njmei]

This ended up being quite a doozy...

Summary of changes:

• Switch to GitHub-actions from now unaccessible Travis CI
• Update starfish dependencies (and fix numerous tests and warnings) Key dependencies that have been bumped up and will be tested by CI include:
  • xarray==0.19.0
  • scikit-image==0.18.3
  • scipy==1.7.1
  • scikit-learn==0.24.2
  • pandas==1.3.2
  • numpy==1.21.2
• Drop python 3.6 support
• Add python 3.9 support

For blow by blow please see individual commit messages. I've tried to organize and add as much useful relevant documentation as possible.

[njmei]

@mattcai @neuromusic @berl Not sure who has the keys (in terms of reviewing PR and deploying) for this repository anymore, but this PR should address quite a few current issues for this project. The biggest being that the existing Travis CI appears to no longer work (and required custom build agents I think).

My fork of this project appears to be passing almost all tests with the exception of two notebooks which run fine on my local machine but appear to be encountering a permissions issue (maybe from trying to download cloudfront data? Maybe something else?) for DARTFISH and SeqFISH notebooks.

To see test status's on my fork see: https://github.com/njmei/starfish/actions/runs/1349929137

Let me know though if my fork is not showing test status though, since it's possible there might be some repo permissions issue!

[berl]

@njmei I am super stoked about this.

... and before I can finish my comment, @ttung swoops in and merges it.

thanks @ttung! now we know you're watching....

[ttung]

It's possible that the data is too big to fit on the github actions machines. They are limited to 7GB RAM / 15GB disk, I believe.

[ttung]

Ok, I fixed the notebooks! Hope you're doing well! :)

[neuromusic]

epic work @njmei!! thanks for the help @ttung :D

[kevinyamauchi]

Wow, this is amazing! Thank you for the update, @njmei and thanks for merging, @ttung !