more work getting rid of csv references

coordinator/ProcessorEnvironment.py

@@ -180,7 +180,7 @@ class ProcessorEnvironment(Processor):
         for region in subregions:
     
             output_dir = f"{jobPath}/plotting/{region.lower()}"
-            csv_template_dir = input_dir + "/{DISEASE_DIR}/RIE_value.nc"
+            rie_template_dir = input_dir + "/{DISEASE_DIR}/RIE_value.nc"
 
             Path(output_dir).mkdir(parents=True, exist_ok=True)
     
@@ -199,16 +199,16 @@ class ProcessorEnvironment(Processor):
                                                       run_params_file_arg = run_config,
                                                       es_output_dir_arg = output_dir,
                                                       issue_date_arg = config['StartString'],
-                                                      disease_csv_template_arg = csv_template_dir)
+                                                      disease_nc_template_arg = rie_template_dir)
     
             env_suit_processor.run_params.FILTER_FOR_COUNTRY = (filter_for_country.upper() == "TRUE")
     
             # Include further diseases in plotting. In this case the irrigated suitabilite for the rusts.
             # TODO: move this part out into a config
             extra_diseases = [
-                EnvSuitDiseaseInfo("Stem rust temp-only", "stem_rust_temponly", config['StartString'], "StemRust_TempOnly", csv_template_dir),
-                EnvSuitDiseaseInfo("Leaf rust temp-only", "leaf_rust_temponly", config['StartString'], "LeafRust_TempOnly", csv_template_dir),
-                EnvSuitDiseaseInfo("Stripe rust temp-only", "stripe_temponly", config['StartString'], "StripeRust_TempOnly", csv_template_dir),
+                EnvSuitDiseaseInfo("Stem rust temp-only", "stem_rust_temponly", config['StartString'], "StemRust_TempOnly", rie_template_dir),
+                EnvSuitDiseaseInfo("Leaf rust temp-only", "leaf_rust_temponly", config['StartString'], "LeafRust_TempOnly", rie_template_dir),
+                EnvSuitDiseaseInfo("Stripe rust temp-only", "stripe_temponly", config['StartString'], "StripeRust_TempOnly", rie_template_dir),
             ]
     
             env_suit_processor.add_diseases(diseases=extra_diseases)

tests/integration/test_suites/env_suit_test_suite.py

@@ -59,13 +59,13 @@ class BaseEnvSuitTestSuite:
             self.assertTrue(eth_file_exists)
 
 
-        def test_standard_run_all_input_csvs_produced(self):
+        def test_standard_run_all_input_ncs_produced(self):
             east_africa_csv_path = os.path.join(IntegrationTestUtils.TEST_OUT_PATH,
                                                 IntegrationTestUtils.TEST_JOB_DIR,
-                                                "plotting", "eastafrica", "input_csvs", "*.nc")
+                                                "plotting", "eastafrica", "input_nc", "*.nc")
             ethiopia_csv_path = os.path.join(IntegrationTestUtils.TEST_OUT_PATH,
                                              IntegrationTestUtils.TEST_JOB_DIR,
-                                             "plotting", "ethiopia", "input_csvs", "*.nc")
+                                             "plotting", "ethiopia", "input_nc", "*.nc")
 
             ea_csv_count: int = IntegrationTestUtils.count_files_in_wildcard(east_africa_csv_path)
             eth_csv_count: int = IntegrationTestUtils.count_files_in_wildcard(ethiopia_csv_path)

tests/integration/test_suites/epi_test_suite.py

@@ -67,7 +67,7 @@ class BaseEpiTestSuite:
             input_csvs_root = os.path.join(IntegrationTestUtils.TEST_OUT_PATH,
                                            IntegrationTestUtils.TEST_JOB_DIR,
                                            "plotting",
-                                           "input_csvs",
+                                           "input_nc",
                                            "*stem*")
 
             self.check_wildcard_exists_and_not_empty(input_csvs_root, ".nc")