♻️ Adapt cli and main tests.

tests/test_cli_integration.py

@@ -26,55 +26,45 @@ def test_ve_run(capsys, mocker):
     """
 
     # import virtual_ecosystem.core  #F401
-    from tests.conftest import patch_bypass_setup, patch_run_update
     from virtual_ecosystem.core.logger import remove_file_logger
     from virtual_ecosystem.entry_points import ve_run_cli
 
-    with (
-        patch_run_update("soil"),
-        patch_bypass_setup("soil") as mock_bypass_setup_soil,
-        patch_run_update("litter"),
-        patch_bypass_setup("litter") as mock_bypass_setup_litter,
-    ):
-        mock_bypass_setup_soil.return_value = False
-        mock_bypass_setup_litter.return_value = False
-
-        with TemporaryDirectory() as tempdir:
-            try:
-                # Install the example directory to run it - tested above - and consume
-                # the resulting stdout
-                ve_run_cli(args_list=["--install-example", tempdir])
-                _ = capsys.readouterr()
-
-                example_dir = Path(tempdir) / "ve_example"
-                configs = example_dir / "config"
-                outdir = example_dir / "out"
-                logfile = outdir / "ve_example.log"
-                ve_run_cli(
-                    args_list=[
-                        str(configs),
-                        "--outpath",
-                        str(outdir),
-                        "--logfile",
-                        str(logfile),
-                        "--progress",
-                    ]
-                )
-
-                # Test the requested --progress output ends as expected
-                captured = capsys.readouterr()
-                expected = "Virtual Ecosystem run complete.\n"
-                assert captured.out.endswith(expected)
-
-                # Check the logfile has been populated as expected
-                assert logfile.exists()
-                with open(logfile) as logfile_io:
-                    contents = logfile_io.readlines()
-                    assert "Virtual Ecosystem model run completed!" in contents[-1]
-
-            except Exception as excep:
-                # If the code above fails then tidy up the logger to restore normal
-                # stream logging rather than leaving all other tests logging to the file
-                # and then fail the test.
-                remove_file_logger()
-                pytest.fail(reason=str(excep))
+    with TemporaryDirectory() as tempdir:
+        try:
+            # Install the example directory to run it - tested above - and consume
+            # the resulting stdout
+            ve_run_cli(args_list=["--install-example", tempdir])
+            _ = capsys.readouterr()
+
+            example_dir = Path(tempdir) / "ve_example"
+            configs = example_dir / "config"
+            outdir = example_dir / "out"
+            logfile = outdir / "ve_example.log"
+            ve_run_cli(
+                args_list=[
+                    str(configs),
+                    "--outpath",
+                    str(outdir),
+                    "--logfile",
+                    str(logfile),
+                    "--progress",
+                ]
+            )
+
+            # Test the requested --progress output ends as expected
+            captured = capsys.readouterr()
+            expected = "Virtual Ecosystem run complete.\n"
+            assert captured.out.endswith(expected)
+
+            # Check the logfile has been populated as expected
+            assert logfile.exists()
+            with open(logfile) as logfile_io:
+                contents = logfile_io.readlines()
+                assert "Virtual Ecosystem model run completed!" in contents[-1]
+
+        except Exception as excep:
+            # If the code above fails then tidy up the logger to restore normal
+            # stream logging rather than leaving all other tests logging to the file
+            # and then fail the test.
+            remove_file_logger()
+            pytest.fail(reason=str(excep))

tests/test_main.py

@@ -12,7 +12,7 @@
 from virtual_ecosystem.core.exceptions import ConfigurationError, InitialisationError
 from virtual_ecosystem.main import ve_run
 
-from .conftest import log_check, patch_bypass_setup, patch_run_update
+from .conftest import log_check
 
 INITIALISATION_LOG = [
     (INFO, "Initialising models: soil"),
@@ -100,23 +100,18 @@ def test_initialise_models(
     core_components = CoreComponents(config)
     caplog.clear()
 
-    with (
-        patch_run_update("soil"),
-        patch_bypass_setup("soil") as mock_bypass_setup,
-    ):
-        mock_bypass_setup.return_value = False
-        with raises:
-            models = initialise_models(
-                config=config,
-                data=dummy_carbon_data,
-                core_components=core_components,
-                models=config.model_classes,
-            )
-
-            if output is None:
-                assert models == [None]
-            else:
-                assert repr(models["soil"]) == output
+    with raises:
+        models = initialise_models(
+            config=config,
+            data=dummy_carbon_data,
+            core_components=core_components,
+            models=config.model_classes,
+        )
+
+        if output is None:
+            assert models == [None]
+        else:
+            assert repr(models["soil"]) == output
 
     log_check(caplog, expected_log_entries)