GitHub Actions CI checks fail due to library updates behind the scenes

[kltm]

Recently, checks for go-site have started failing with errors like:

Run python3 ./scripts/sanity-check-users-and-groups.py --verbose --users metadata/users.yaml --groups metadata/groups.yaml
INFO:sanity:Verbose: on
INFO:sanity:Will operate on users: metadata/users.yaml
INFO:sanity:Will operate on groups: metadata/groups.yaml
Traceback (most recent call last):
  File "./scripts/sanity-check-users-and-groups.py", line 191, in <module>
    main()
  File "./scripts/sanity-check-users-and-groups.py", line 70, in main
    users = yaml.load(mhandle.read())
TypeError: load() missing 1 required positional argument: 'Loader'
Error: Process completed with exit code 1.

This seems to be caused by a change in PyYAML (a la bioconda/bioconda-utils#462 yaml/pyyaml#576) that changes how the loader needs to be used.

Tagging @ValWood (who was first bitten) and @sierra-moxon (as libraries sloshing around and upgrading themselves has been an ongoing issue in many projects).

[kltm]

Same issue in sparta it seems...

[kltm]

I believe this can generally be solved with yaml.load -> yaml.safe_load.

[kltm]

Well, after a very frustrating morning of chasing things down, I believe with the above passing we are good again.
@dustine32 @sierra-moxon Please let me know if other things crop up like this--I want to build up an argument for locked versions > free floating versions.

[dustine32]

@kltm Way to go! Yeah, I think "locked versions > free floating versions" works well for go-site since it's pretty much only used by us (GO (I think?)). To contrast, I know users of ontobio have certainly favored unpinning or at least only pinning min versions (see biolink/ontobio#482). Personally, I've been bitten by both approaches so *shrug emoji*.