Standardise stochastics

[weshinsley]

Ok, this is a mess of a PR as the more code I wrote, the more issues I found that needed fixing.

The point of the PR is:-

• Two files, stochastic_files.R and stochastic_graphs.R - the first converts from the incoming (drop)box files to a format that hopefully we'll like - pq files we can load with arrow::read_parquet - and they are standardised in a way that's nice. For example usage, see scripts/process_stoch_202310gavi.R and scripts/process_stoch_202409malaria.R which I used to generate the data you may have seen.

The rest of the PR is not really very interesting and sorts out a bunch of other things.

• The CI had not been run for a while and was failing, so the contents of .github/workflows are taken from more recent R projects that have CI.

• We used to use the qs format for the aggregated data that would get pushed to annex - and is also in some reports containing that same aggregated data. Sadly, the qs package has been dumped, and the qs2 that supercedes it is not compatible with the original - it can't read the old files. This is quite disappointing, and since we are using pq in other places, I've gone with arrow throughout, in the hope that will last longer. I'll revisit the reports at some point.

• The new code is tested with 100% coverage! Hurrah. But also some older tests needed fixing - some because testthat has changed some of its output text, and some were missing from some previous work to do with expressing outcomes as a list of whatever the outcomes are, rather than explicitly being deaths, cases and dalys. (We wanted to add ylls).

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 100.00%. Comparing base (b5547b8) to head (3b9a955).
⚠️ Report is 8 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff            @@
##            master       #34   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
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  Files           20        22    +2     
  Lines         2329      2399   +70     
=========================================
+ Hits          2329      2399   +70     

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