OAK dependency tuning

[hrshdhgd]

• Addresses comment on Improve usage of SSSOM-py #666

• Addresses Check dependencies in pyproject.toml #323

• Limited sssom to < 0.4.0

• Removed unnecessary sssom-schema dependency since it is satisfied by sssom itself.

• Removed lark dependency (Unsure how it got in there)

• Added linkml as a dependency in tox for running tests.

• Removed semsimian fixed version dependency.

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (be57506) 76.48% compared to head (2aff610) 76.48%.

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Additional details and impacted files

@@           Coverage Diff           @@
##             main     #686   +/-   ##
=======================================
  Coverage   76.48%   76.48%           
=======================================
  Files         252      252           
  Lines       29386    29386           
=======================================
+ Hits        22475    22477    +2     
+ Misses       6911     6909    -2     

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[cmungall]

In general I favor less pinning but given how tightly coupled these are, I think limiting to 0.2.* may be sensible? See also Mark's Q in #oak

[hrshdhgd]

ok, switched to ^0.2.1. As per Mark's Q, I did read it and it was confusing with the versions he mentioned.

[cmungall]

a bit worried about duplication of dependency metadata but I don't quite understand why these are in tox.ini in the first place

[hrshdhgd]

This is because if we run tox -e py (to run pytest via tox), it throws errors about linkml module not found (in tot's virtual environment). It doesn't affect poetry and it's working in general. We could do away with tox and be solely poetry dependent but we've had those conversations in the past.