making the Processor.py pass on non-zero exit codes when exiting - I THINK THIS COULD CAUSE PROEBLEMS WITH INTEGRATION TESTS, AS IT WILL EXIT THE PYTHON ENVIRONMENT RATHER THAN CARRYING ON TO THE ASSERTS IF THERE IS AN ERROR, WILL ROLE BACK IF THIS IS THE CASE

fixing env suit half fat test (fewer output files now we have switched to using the mean of daily max as standard for env suit)

removing unused spatial points file from function signature and changing variable name to reflect that filtering is no longer happening

...in recent commits to ews-coordinator and ews-epidemiology.

This is done with a set of <date_valid_from>: <host_file.tif> pairs in
the run configuration under ['Epidemiology']['Host']['HostRasters'].
This is an optional argument. The 'HostRaster' argument in the
configuration is still needed, but is renamed as 'TargetRaster' to
avoid confusion.

Cocnurrent changes were made in epi model.

This may one day be replaced by some 'host preprocessing' type
of EWS component.

Aspects to improve:

*  Currently, the dynamic host map has to be handled both in
ews-epidmiology for run time, and here for post-run in order
to convert units. It might be neater to do once in one place only
 by moving the unit conversion functionality into the epi model.

 * Implement testing for handling of dynamic host data.

See EpiModel.EpiPrep.updater.update_input() docstring for comments.

This should substantially speed up production epi runs, particularly
towards the end of the season.

This commit also unifies deposition and env suit preparation code.

Not for immediate production, awaiting verification from Yoseph.

Credentials to access the new survey form are available on episerver at
/storage/app/EWS_prod/regions/EastAfrica/resources/coordinator/configs/
Cred-ODK-EIAR_newODK.json

changing the landpoint files to use a new column "included", to filter for countries, rather than using the lat lon values to decide what to filter

Adding the functionality to group surveys and run source gen on each groups. Grouping is only run if it is defined in the config (otherwise it use all available surveys), and it is based on the 'Origin' column of the surveys. All unique 'Origin' will create its own group alongside the ones defined in the config. Groups can be ignored by defining 'GroupsToIgnore' in the config (this has no effect on 'Origin' types).

The model outputs were clipped to a smaller extent but the host map was
not. Because the epi model run grid is set by the host map, there is a big
time-saving by moving to a clipped host map. The epi partial integration
test passed on my machine, so now to check it passes in gitlab CI
pipeline.

Handle missing redundant columns and continue to set a common column
order at the same time.

This is useful for the new ODK form until the wheat rust toolbox is setup.

adding a page to the documentation for the setup of the IaaS server (not linked from within the docs)

changing the example landpoint files to be sorted lon,lat as the sort order gets enforced by the landpoint filter functions in postprocessing now.