Update linkml and linkml-runtime dependencies

[amc-corey-cox]

The linkml and linkml-runtime dependencies appear to be pinned to some pretty old versions. We should update these to the current versions. This may solve an issue I'm having with windows-latest failing as well.

[amc-corey-cox]

No this doesn't resolve the windows failures... it also causes a lot of other breakage. I'm tabling this for now.

[amc-corey-cox]

These are fixed in #165