Deduplication inchi check vs aromaticity

[lilyminium]

The deduplication check hashes molecules via inchikey, then tries to remap them via an isomorphism check. Unfortunately structures like the below have the same inchikey, but different bond orders/aromaticity perception, so this raises an assertion error here: https://github.com/openforcefield/openff-qcsubmit/blob/2fa465a87ffea4c5b02d5d0cd8622d1a22d4fe83/openff/qcsubmit/workflow_components/utils.py#L713-L723

In this particular case, adding aromatic_matching=False to the are_isomorphic check did fix it for me.

[jthorton]

Ah another one for the ever-growing list of deduplication edge cases which is where the formal charge and bond order matching settings come from. I think your solution should be fine generally as this check is only ran if the inchi matches!

[mattwthompson]

This is hopefully caught by #260