adding file-based logging to epi fit (to allow different configuration when running in gitlab-ci)

.gitlab-ci.yml

@@ -147,20 +147,20 @@ epi_fit:
       export LOGGING_CONFIG_FILE_PATH
       
       mkdir $CI_PROJECT_DIR/fitting_outputs
-
-      cp -rv $OUTPUT_DIR/*.csv $OUTPUT_DIR/*.json $OUTPUT_DIR/parameter_sweep_heatmaps $CI_PROJECT_DIR/fitting_outputs/
-
+      
+      python3 $PACKAGES_DIR/epimodel/ews/epi_model/fit_lb584.py
+      /storage/app/EWS_prod/regions/EastAfrica/test_workspace/integration/epi_fit/dev/data_proc/6.0_epi_pipeline/inputs/configs/sys_config_epi_remote.json
+      /storage/app/EWS_prod/regions/EastAfrica/test_workspace/integration/epi_fit/dev/data_proc/6.0_epi_pipeline/inputs/configs/run_config_epi_long_remote.json
+      $OUTPUT_DIR
+      2016
+      
       python3 $PACKAGES_DIR/epimodel/ews/epi_model/epi_fit/params_metrics_file_compare.py       
+
       /storage/app/EWS_prod/regions/EastAfrica/test_workspace/integration/epi_fit/dev/outputs/optimum_parameters_metrics.csv 
       /storage/app/EWS_prod/regions/EastAfrica/test_workspace/integration/epi_fit/dev/data_proc/6.0_epi_pipeline/inputs/configs/example_optimum_parameters_metrics.csv 
-
-      exit_code=$?
-      echo "Exit code: $exit_code"
+      /storage/app/EWS_prod/regions/EastAfrica/test_workspace/integration/epi_fit/dev/outputs/metric_comparison.txt
       
-      if [ $exit_code -ne 0 ]; then
-        echo "Parameter metrics comparison failed"
-        exit 1
-      fi
+      cp -rv $OUTPUT_DIR/*.csv $OUTPUT_DIR/*.json $OUTPUT_DIR/*.txt $OUTPUT_DIR/parameter_sweep_heatmaps $CI_PROJECT_DIR/fitting_outputs/
 
   artifacts:
     when: always