Fixes to type annotations and test configurations

[nsoranzo]

Ping @lldelisle

[nsoranzo]

The pytest failures are currently expected, will work on that next.

[lldelisle]

Do we really need to lint on both python version?

[nsoranzo]

Do we really need to lint on both python version?

IMO yes, it costs us 15s and it's not a change from the previous setup.

[lldelisle]

Looks good to me but I am not sure to be the more competent person...

[nsoranzo]

The pytest failures are currently expected, will work on that next.

I have a fix for this, will open a PR to galaxy's release_25.1 branch tomorrow, but this PR can be merged in the mean time.

[nsoranzo]

The pytest failures are currently expected, will work on that next.

I have a fix for this, will open a PR to galaxy's release_25.1 branch tomorrow, but this PR can be merged in the mean time.

galaxyproject/galaxy#21753

[mvdbeek]

just merge the galaxy pr, thank you!

[nsoranzo]

I think we need updated 25.1 Galaxy packages for the tests to pass.