Add a wrapping CLI so that researchers don't need to touch Python if they don't want to.
This CLI currently only offers one subcommand: accuracy which does the 3-way accuracy calculation from paper.py in the covid folder. :shrug: it seemed like a reasonable place to start, but we should talk about what top-level operations make sense.
Add some very brief initial unit tests (just one method right now)
Biggest change is converting the config file format from Python to Yaml/Json
Researchers will touch this, so static config is easier to understand/explain and there's less room to shoot yourself in the foot
It's awkward to import arbitrary Python from a random project dir safely/wisely
I'm generally preferring Yaml where possible because you can have comments in it, but config.json will work too.
Bumped minimum python to 3.10 -- just for convenience of using some nicer type hinting it has. (Cumulus ETL requires 3.10, so this doesn't seem crazy to me)
I've split this PR up into different commits, which should hopefully make it easier to read. But there's still a fair bit.
OK on my first pass at interacting with the chart-review code, I wrote down some possible improvements here: https://github.com/smart-on-fhir/chart-review/issues/1
This is the PR to solve them. Specifically:
accuracywhich does the 3-way accuracy calculation frompaper.pyin the covid folder. :shrug: it seemed like a reasonable place to start, but we should talk about what top-level operations make sense.config.jsonwill work too.I've split this PR up into different commits, which should hopefully make it easier to read. But there's still a fair bit.