Add NPI activation triggers to Gleam simulations

Description

We want to be able to plot simulations with NPIs triggered by the current situation.

NPI triggers are:

Number of deaths in the last N days (e.g. N=14)
Number of infections in the last N days (e.g. N=14) with different limits for activation and deactivation.

The NPIs do not have to be concrete, only the R reduction (resp. beta reduction) matters.

(User interface has some details fleshed out)

Have 4 levels of NPIs (0-3), where 0 is initial and has the refault R.
Let forecasters generate estimates for trigger limits for all levels, and the R reduction factor, for each country.
Forecasters input those into spreadsheet (google sheet), for any number of countries (or areas), downloaded as CSV
Repeat cca 4 times (more is fine), starting with no triggered NPIs in the input spec file:
- Run the model in Gleam with the latest batch file, import results into the batch file
- Create a new batch file with 0-1 triggered NPI added for each country
- For each country, see if some new trigger would be activated after the last one was
- If so, add a new setting for beta (dep. on R reduction) into the XML def starting at that date
- A new table triggered_NPIs in the batch HDF5 file is used to store which NPI levels are activated and when (hard to distinguish them from the exceptions in the XMLs)
- Existing trigger activations get never modified, even if they would shift for some reason (randomness, migration from other country)
- The sequence data is copied to the new batch file but truncated (relaced by NaNs) after when the new intervention would be added - so that we ca nuse it directly for web export and only have valid data there.

The steps are marked [old] if they are exactly the same as without triggers, [new] if new or modified.

[old] Create the HDF5 file A0.hdf5 (example name) with scenarios with GenerateGleamBatch as usual (from base def XML, infections, ...)
[old] Export the definitions in A0.hd5 to GLEAM with ExportSimulationDefinitions
[old] Run GLEAM for the exported simulations
[old] Import simulation results with ExtractSimulationsResults into A0.hdf5
[new] Download the triggers spreadsheet as CSV, (example name triggers.csv)
[new] Create batch file A1.hdf5 from A0.hdf5 and triggers.csv with UpdateBatchTriggers (new task)
- This reports when the new triggers are added and for how many countries
- After this, A1 trajectories are same as in A0 but truncated (with NaNs or -1) after the newly added trigger (as they are invalid).

Repeat few times (suggestion: 3) for N=1,2,3,...

[old] Export the definitions in A(N).hd5 to GLEAM with ExportSimulationDefinitions
[old] Run GLEAM for the exported simulations
[old] Import simulation results with ExtractSimulationsResults into A(N).hdf5
[new] Create batch file A(N+1).hdf5 from A(N).hdf5 and triggers.csv with UpdateBatchTriggers (new task)
- This reports when the new triggers are added and for how many countries
- After this, A(N+1) trajectories are same as in A(N) but truncated (with NaNs or -1) after the newly added trigger (as they are invalid).

Then:

Each subsequent trigger added for one country may influence development in other countries that already added trigger far in future. This should not be a big shift, I would ignore it.
Having the deactivation limit too close to activation may trigger fast on-off cycle, requiring a lot of gleam repeats.
The triggers activate for the actual number of infections, not observed. The forecasters need to take this into account.