reconcile recent branches

[turbomam]

New stuff for DataGood: example of extracting terms for owl with robot; black formatting #51

https://github.com/microbiomedata/sample-annotator/pull/51/files

vs

E ModuleNotFoundError: No module named 'report_model'

[turbomam]

fresh clone of main in [email protected]:microbiomedata/sample-annotator.git

make all works up to

poetry run annotate-sample -R examples/outputs/report.tsv examples/gold.json

OSError: Cannot save file into a non-existent directory: 'examples/outputs'

see also #50

[turbomam]

pushed examples/outputs/placeholder.txt and make all completes now but doesn't include sample_annotator/clients/biosample_sqlite_client.py

note examples/outputs/placeholder.txt seems to get deleted by make clean now

[turbomam]

make clean doesn't rm examples/outputs/placeholder.txt any more now

[turbomam]

I still don't understand if we are supposed to be importing Message from either .sample_annotator or report_model

both error out and make all succeeds when they are both commented out

[turbomam]

does anything actually use utils/flatten.py ?