dropping the return of plotting outputs as not needed now we use workflow manager

ews/coordinator/processor_epidemiology.py

@@ -553,26 +553,6 @@ class ProcessorEpidemiology(ProcessorBase):
                     logger.debug('Saving tif output as png for easier viewing')
                     plotRaster.save_raster_as_png(outfile)
 
-            # comparison figure
-
-            # TODO: make this plot configurable? with function or args?
-            #logger.info('Plotting epi output alongside contributing components')
-            # figure_func = getattr(EpiAnalysis,'plot_compare_host_env_dep_infection')
-            logger.info('Plotting composite image of epi formulations')
-            figure_func = getattr(EpiAnalysis, 'plot_compare_epi_cases')
-
-            # isolate the config for this function, in case of modifications
-            config_epi_for_comparison = config.copy()
-
-            fig,axes,cases = figure_func(
-                    config_epi_for_comparison,
-                    start_str = start_string,
-                    end_str = end_string)
-
-            SaveFileName = f"{case_specific_path}/EPI_{config_filename}_comparison"
-
-            fig.savefig(SaveFileName+'.png',dpi=300)
-
             # slice the epi results into before forecast and in forecast
 
             for epiconf in config['Epi']:
@@ -633,8 +613,8 @@ class ProcessorEpidemiology(ProcessorBase):
 
         return proc_out
 
-    def process_EWS_plotting_epi(self, jobPath,config) -> [str]:
-        '''Returns a list of output files for transfer.'''
+
+    def process_EWS_plotting_epi(self, job_path, config):
 
         logger.info('started process_EWS_plotting_epi()')
 
@@ -676,7 +656,7 @@ class ProcessorEpidemiology(ProcessorBase):
         # TODO: handle multiple diseases and regions in Processor as a loop, or in the config
         deposition_disease_name = [disease_latin_name_dict[disease]+'_DEPOSITION' for disease in diseases][0]
 
-        ews_plot_dir = f"{jobPath}/plotting/"
+        ews_plot_dir = f"{job_path}/plotting/"
 
         Path(ews_plot_dir).mkdir(parents=True, exist_ok=True)
 
@@ -758,11 +738,6 @@ class ProcessorEpidemiology(ProcessorBase):
                 logger.error('EWS-Plotting did not produce any output')
                 raise RuntimeError
 
-        # provide to list for transfer
-        ews_plotting_outputs: [str] = [item for ews_plotting_output in ews_plotting_output_globs for item in glob(ews_plotting_output)]
-
-        return ews_plotting_outputs
-
 
 if __name__ == '__main__':
     processor = ProcessorEpidemiology()