resolve unit tests failing after recent changes

scripts/runResistnet.py

@@ -6,7 +6,6 @@
 from resistnet.params import parseArgs
 from resistnet.resistance_network import ResistanceNetwork
 from resistnet.model_optimisation import ModelRunner
-# from resistnet.samc_network import ResistanceNetworkSAMC
 
 
 def main():
@@ -21,27 +20,7 @@ def main():
         params.seed = datetime.now().timestamp()
     random.seed(params.seed)
 
-    # Step 1: Initialise network data
-    # network = ResistanceNetworkSAMC(
-    #     network=params.network,
-    #     shapefile=params.shapefile,
-    #     sizes=params.sizefile,
-    #     coords=params.coords,
-    #     variables=params.variables,
-    #     agg_opts=params.agg_opts,
-    #     pop_agg=params.pop_agg,
-    #     inmat=params.inmat,
-    #     reachid_col=params.reachid_col,
-    #     length_col=params.length_col,
-    #     infer_origin=params.infer_origin,
-    #     origin=params.origin,
-    #     rtol=params.rtol,
-    #     solver=params.solver,
-    #     max_iter=params.max_iter,
-    #     max_fail=params.max_fail,
-    #     out=params.out,
-    #     verbose=True
-    # )
+    # Step 1: Initialise network
     network = ResistanceNetwork(
         network=params.network,
         shapefile=params.shapefile,
@@ -105,7 +84,6 @@ def main():
         verbose=True
     )
 
-
 # Call main function
 if __name__ == '__main__':
     os.environ['USE_PYGEOS'] = '0'

src/resistnet/params.py

@@ -366,9 +366,6 @@ def display_help(self, message=None):
             "    -b, --burn: Number of generations for pre-burnin [def.=0]\n"
             "    --max_hof_size: Maximum models retained [default=100]\n\n"
 
-            "SAMC options:\n"
-            "Not currently implemented\n\n"
-
             "Multi-model inference options:\n"
             "    -a, --awsum: Cumulative Akaike weight threshold [def.=0.95]\n"
             "    --use_full: Use full rather than natural model averaging\n"

tests/resistnet/test_model_optimisation.py

@@ -14,10 +14,8 @@ def ga_parameters_fixture():
         'indpb': 0.05,
         'popsize': 10,
         'maxpopsize': 10,
-        'posWeight': True,
         'fixWeight': False,
         'fixShape': True,
-        'allShapes': False,
         'min_weight': 0.5,
         'max_shape': 2.0,
         'max_hof_size': 100,
@@ -119,10 +117,8 @@ def test_model_runner_initialization(resistance_network_fixture):
     assert model_runner.indpb is None
     assert model_runner.popsize is None
     assert model_runner.maxpopsize is None
-    assert model_runner.posWeight is None
     assert model_runner.fixWeight is None
     assert model_runner.fixShape is None
-    assert model_runner.allShapes is None
     assert model_runner.min_weight is None
     assert model_runner.max_shape is None
     assert model_runner.max_hof_size is None

tests/resistnet/test_params.py

@@ -30,7 +30,7 @@ def test_display_help_called():
 def test_parse_args_conflicting_weight_options():
     test_args = [
         "script_name", "-o", "my_prefix", "-g", "genmat_file",
-        "--shp", "shapefile.shp", "--posWeight", "--fixWeight",
+        "--shp", "shapefile.shp", "--fixWeight",
         "-v", "example1,example2,example3"]
     sys.argv = test_args
 
@@ -92,9 +92,7 @@ def test_parse_args_defaults():
     assert args.modavg is True
     assert args.report_all is False
     assert args.plot is True
-    assert args.posWeight is False
     assert args.fixWeight is False
-    assert args.allShapes is False
     assert args.fixShape is False
     assert args.max_shape == 100
     assert args.min_weight == 0.0
@@ -106,7 +104,7 @@ def test_parse_args_nondefaults():
         "--shp", "shapefile.shp", "-v", "example1", "-P", "123",
         "-G", "123", "--threads", "4", "-d", "0.001", "-D", "0.01",
         "-F", "42", "-T", "42", "--cxpb", "0.42", "--indpb", "0.42",
-        "--mutpb", "0.42", "--burn", "2", "--posWeight", "--report_all",
+        "--mutpb", "0.42", "--burn", "2", "--report_all",
         "-o", "example", "--awsum", "0.42", "--max_hof_size", "123",
         "--min_weight", "0.042", "--max_shape", "42"
     ]
@@ -133,9 +131,7 @@ def test_parse_args_nondefaults():
     assert args.modavg is True
     assert args.report_all is True
     assert args.plot is True
-    assert args.posWeight is True
     assert args.fixWeight is False
-    assert args.allShapes is False
     assert args.fixShape is False
     assert args.max_shape == 42
     assert args.min_weight == 0.042

tests/resistnet/test_resistance_network.py

@@ -207,9 +207,7 @@ def test_resistance_network_worker_creation(resistance_network_fixture):
         'gendist': resistance_network_fixture._gendist,
         # Use defaults or specific values for the additional attributes
         'fitmetric': 'aic',
-        'posWeight': False,
         'fixWeight': False,
-        'allShapes': False,
         'fixShape': False,
         'min_weight': 0.0,
         'max_shape': 100.0
@@ -227,9 +225,7 @@ def test_resistance_network_worker_creation(resistance_network_fixture):
 
     # Validate unique attributes for ResistanceNetworkWorker
     assert worker.fitmetric == 'aic'
-    assert worker.posWeight is False
     assert worker.fixWeight is False
-    assert worker.allShapes is False
     assert worker.fixShape is False
     assert worker.min_weight == 0.0
     assert worker.max_shape == 100.0