add TB culture HSI

[tdm32]

This branch has the HTM scale-up scenarios plus the new culture diagnostic test for tb which is used for people with a false test (xpert, sputum, xray or clinical) but all the symptoms indicative of tb. It is only called if program scale-up is 'target' or 'max'

[tbhallett]

Thanks Tara -- running now.

For the review, maybe we should allow this to happen only under 'max', since we think it's quite hypothetical?

[tdm32]

Thanks Tara -- running now.

For the review, maybe we should allow this to happen only under 'max', since we think it's quite hypothetical?

Sure. I think it will depend on what we want to present, are you thinking that we only present the max scenario? The targeted scenario will likely show a very muted effect.

[tbhallett]

Thanks @tdm32 --- do we want to roll-back the analysis scripts on here, so that it's just the changes to the TB module....? Or, are you using this for your production runs for your current GF and FCDO analyses?

[tdm32]

Thanks @tdm32 --- do we want to roll-back the analysis scripts on here, so that it's just the changes to the TB module....? Or, are you using this for your production runs for your current GF and FCDO analyses?

@tbhallett I've rolled back those files which do exist on master. Additional analysis scripts on this branch - which are not present in master - don't need to be pushed. Should we delete them or can we just merge those relevant files?

Required for merge to master:
resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES.xlsx
src/tlo/methods/tb.py

[tbhallett]

Are we keeping this or closing it off? @tdm32

[tbhallett]

@tdm32 on this one:

• there are lots of script file from the FCDO/GF analysis bundled in here, that I presume we don't want to come in on this PR. I believe the only changes needed are in tb.py. If so, please roll back the others\

• I see that with the last merge in of master, there were failing tests -- so after that fix, we'll need to wait for the test to pass.

[tbhallett]

I don't see where the option to suppress the footprint is exercised? Just checking if it should be, given that you've put this logic in?

Also - no need for the else clause: no return, implies that ( return ACTUAL_APPT_FOOTPRINT) anyway and Is quicker.

[tdm32]

I've removed this now

[tbhallett]

@tdm32 --- I've removed the files that I think didn't want to be on this PR. The .xlsx for Priority Polices look the same to me? Are you sure we need to update?

[tdm32]

@tdm32 --- I've removed the files that I think didn't want to be on this PR. The .xlsx for Priority Polices look the same to me? Are you sure we need to update?

@tbhallett there should be the additional HSI for TB culture in the priority policies sheets