fix for config.general.show_nested_entities

[pisong314]

The issue
whether the config.general.show_nested_entities flag is True or False, there seems to be no effect to the output.

Example
if the text is “chest pain” which matches 1) “chest pain” greedily 2) “chest” 3) “pain”, it seems to produce all 3 entities at the end at all time regardless of the flag.

What's wrong

• the current logic in postprocessing.py doesn't seem to be filtering anything.
• the filtering logic doesn't appear to look at the flag at all.

The fix

• re-implementation of the filtering logic to simply use token index to filter.
• the flag is passed on and checked during post-processing.

[mart-r]

Thank you for the contribution! Much appreciated!

This was handled somewhat differently on v1, but I do think this approach makes a lot of sense!

And kudos for the actual unit tests!

[mart-r]

Just the changes from the workflow needed.

[pisong314]

I just added # type: ignore from the original code back. seems to build ok now.

[pisong314]

The failing bit now seems to be due to that I don't have access to your environment variables.

[mart-r]

Yes. Don't worry about that. All good otherwise.

[pisong314]

thanks!