Ci fixes

bionetgen/modelapi/bngfile.py

@@ -84,11 +84,9 @@ def generate_xml(self, xml_file, model_file=None) -> bool:
                     xml_file, stripped_bngl
                 )  # no need to chdir here, handled by finally block
 
-            app_stdout = conf.get("stdout")
-            app_suppress = False if app_stdout == "STDOUT" else self.suppress
             rc, _ = run_command(
                 ["perl", self.bngexec, "--xml", stripped_bngl],
-                suppress=app_suppress,
+                suppress=self.suppress,
                 cwd=temp_folder,
             )
             if rc != 0:

tests/test_csimulator.py

@@ -189,8 +189,10 @@ def test_csimulator_init_str():
     with unittest.mock.patch(
         "bionetgen.simulator.csimulator._new_ccompiler"
     ) as mock_new_comp:
-        with unittest.mock.patch("bionetgen.simulator.csimulator.conf") as mock_conf:
-            mock_conf.get.return_value = "dummy"
+        with unittest.mock.patch(
+            "bionetgen.simulator.csimulator.get_conf"
+        ) as mock_conf:
+            mock_conf.return_value = {"cvode_include": "dummy", "cvode_lib": "dummy"}
 
             with unittest.mock.patch(
                 "bionetgen.simulator.csimulator.bionetgen.run"
@@ -222,8 +224,10 @@ def test_csimulator_init_bngmodel():
     with unittest.mock.patch(
         "bionetgen.simulator.csimulator._new_ccompiler"
     ) as mock_new_comp:
-        with unittest.mock.patch("bionetgen.simulator.csimulator.conf") as mock_conf:
-            mock_conf.get.return_value = "dummy"
+        with unittest.mock.patch(
+            "bionetgen.simulator.csimulator.get_conf"
+        ) as mock_conf:
+            mock_conf.return_value = {"cvode_include": "dummy", "cvode_lib": "dummy"}
 
             with unittest.mock.patch(
                 "bionetgen.simulator.csimulator.bionetgen.run"

tests/test_modelapi_export_errors.py

@@ -226,6 +226,13 @@ def test_bngmodel_passes_path_options_to_bngparser(mock_parser_cls):
     from bionetgen.modelapi.model import bngmodel
 
     parser = MagicMock()
+
+    def _fake_parse_model(model):
+        for b in model._block_order:
+            if b not in model.active_blocks:
+                model.active_blocks.append(b)
+
+    parser.parse_model.side_effect = _fake_parse_model
     mock_parser_cls.return_value = parser
 
     bngmodel(
@@ -240,6 +247,7 @@ def test_bngmodel_passes_path_options_to_bngparser(mock_parser_cls):
         BNGPATH="/custom/bng",
         generate_network=True,
         suppress=False,
+        verbose=False,
     )
     parser.parse_model.assert_called_once()