modify ref instead of output

tests/conftest.py

@@ -15,27 +15,28 @@ def pytest_addoption(parser):
         help="Directory for (only-read) inputs for tests",
     )
     parser.addoption(
-        "--simulate-gpu",
+        "--no-gpu",
         action="store_true",
-        help="""To simulate the presence of a gpu on a cpu-only device. Default is False.
+        help="""To run tests on cpu. Default is False.
             To use carefully, only to run tests locally. Should not be used in final CI tests.
-            Concretely, the tests won't fail if gpu option if false in the output MAPS whereas
-            it should be true.""",
+            Concretely, the tests won't fail if gpu option is false in the output MAPS whereas
+            it is true in the reference MAPS.""",
     )
     parser.addoption(
         "--adapt-base-dir",
         action="store_true",
-        help="""To virtually change the base directory in the paths stored in MAPS. Default is False.
+        help="""To virtually change the base directory in the paths stored in the MAPS of the CI data.
+            Default is False.
             To use carefully, only to run tests locally. Should not be used in final CI tests.
-            Concretely, the tests won't fail if only the base directory differs in the paths stored
-            in the MAPS.""",
+            Concretely, the tests won't fail if only the base directories differ in the paths stored
+            in the output and reference MAPS.""",
     )
 
 
 @pytest.fixture
 def cmdopt(request):
     config_param = {}
     config_param["input"] = request.config.getoption("--input_data_directory")
-    config_param["simulate gpu"] = request.config.getoption("--simulate-gpu")
-    config_param["adapt base dir"] = request.config.getoption("--adapt-base-dir")
+    config_param["no-gpu"] = request.config.getoption("--no-gpu")
+    config_param["adapt-base-dir"] = request.config.getoption("--adapt-base-dir")
     return config_param

tests/test_train_ae.py

@@ -88,7 +88,7 @@ def test_train_ae(cmdopt, tmp_path, test_name):
     else:
         raise NotImplementedError(f"Test {test_name} is not implemented.")
 
-    if cmdopt["simulate gpu"]:
+    if cmdopt["no-gpu"]:
         test_input.append("--no-gpu")
 
     if tmp_out_dir.is_dir():
@@ -104,16 +104,16 @@ def test_train_ae(cmdopt, tmp_path, test_name):
 
     if test_name == "patch_multi_ae":
         json_data_out["multi_network"] = True
-    if cmdopt["simulate gpu"]:
-        json_data_out["gpu"] = True
-    if cmdopt["adapt base dir"]:
+    if cmdopt["no-gpu"]:
+        json_data_ref["gpu"] = False
+    if cmdopt["adapt-base-dir"]:
         base_dir = base_dir.resolve()
         ref_base_dir = Path(json_data_ref["caps_directory"]).parents[2]
-        json_data_out["caps_directory"] = str(
-            ref_base_dir / Path(json_data_out["caps_directory"]).relative_to(base_dir)
+        json_data_ref["caps_directory"] = str(
+            base_dir / Path(json_data_ref["caps_directory"]).relative_to(ref_base_dir)
         )
-        json_data_out["tsv_path"] = str(
-            ref_base_dir / Path(json_data_out["tsv_path"]).relative_to(base_dir)
+        json_data_ref["tsv_path"] = str(
+            base_dir / Path(json_data_ref["tsv_path"]).relative_to(ref_base_dir)
         )
     assert json_data_out == json_data_ref  # ["mode"] == mode