Renaming function and adjusting unit test

flepimop/gempyor_pkg/src/gempyor/seir.py

@@ -16,7 +16,7 @@
 logger = logging.getLogger(__name__)
 
 # TO DO: Write documentation for this function
-def neg_params(
+def check_parameter_positivity(
         parsed_parameters: np.ndarray, 
         parameter_names: list[str], 
         dates: pd.DatetimeIndex, 
@@ -160,7 +160,7 @@ def build_step_source_arg(
         "stochastic_p": modinf.stoch_traj_flag,
     }
 
-    neg_params(
+    check_parameter_positivity(
         fnct_args["parameters"],
         modinf.parameters.pnames,
         modinf.dates,

flepimop/gempyor_pkg/tests/seir/test_seir.py

@@ -17,19 +17,14 @@
 DATA_DIR = os.path.dirname(__file__) + "/data"
 os.chdir(os.path.dirname(__file__))
 
-def test_neg_params():
-
-    config.set_file(f"{DATA_DIR}/config.yml")
-    modinf = model_info.ModelInfo(
-        config=config,
-        nslots=1,
-        seir_modifiers_scenario="None",
-        write_csv=False,
-    )
-
-    parameter_names = modinf.parameters.pnames
-    dates = modinf.dates
-    subpop_names = modinf.subpop_pop
+def test_check_parameter_positivity():
+
+    parameter_names = ['alpha*1*1*1', 'sigma_OMICRON*1*1*1', '3*gamma*1*1*1', 'epsilon+omegaph4*1*1*1', 
+                       '1*zeta*1*1', 'r0*gamma*theta10*1*chi_OMICRON*1', 'r0*gamma*theta9*1*chi_OMICRON*1', 
+                       'eta_X0toX3_highIE*1*1*nuage0to17', 'eta_X0toX3_highIE*1*1*nuage18to64LR', 
+                       'eta_X0toX3_highIE*1*1*nuage18to64HR', 'eta_X0toX3_highIE*1*1*nuage65to100',]
+    dates = pd.date_range('2023-03-19', '2025-04-31', freq="D")
+    subpop_names = ['56000', '50000', '11000', '02000', '38000', '46000', '10000', '30000', '44000', '23000']
 
     # Test case 1: no negative params
     test_array1 = np.zeros((len(parameter_names)-1, len(dates)-1, len(subpop_names)-1))