splitting out some csv parsing functions

splitting out some csv parsing functions

splitting out some csv parsing functions

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)

...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.

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

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.

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

changing the optional SPATIAL_POINTS_FILE config parameter to SPATIAL_POINTS_FILE_TEMPLATE and allowing ${} value subsiitution in the paremeter value
removing some points from the ethiopia post processing landpoint file, to allow checking that the filtering for post-processing is working

allowing the full iontegration pipeline for Surveys to use the standard deployment config, rather than trying to exclude WRSIS