update unit tests

tests/integration/data/nplinker_local_mode.toml

@@ -1,7 +1,17 @@
-dynaconf_merge = true # merge with the default settings, provided by the Dynaconf library
-
 root_dir = "@format {env[NPLINKER_ROOT_DIR]}"
 mode = "local"
 
 [log]
 level = "DEBUG"
+use_console = true
+
+[mibig]
+to_use = true
+version = "3.1"
+
+[bigscape]
+version = 1
+cutoff = "0.30"
+
+[scoring]
+methods = ["metcalf"]

tests/unit/data/nplinker_local_mode.toml

@@ -1,7 +1,17 @@
-dynaconf_merge = true # merge with the default settings, provided by the Dynaconf library
-
 root_dir = "@format {env[NPLINKER_ROOT_DIR]}"
 mode = "local"
 
 [log]
 level = "DEBUG"
+use_console = true
+
+[mibig]
+to_use = true
+version = "3.1"
+
+[bigscape]
+version = 1
+cutoff = "0.30"
+
+[scoring]
+methods = ["metcalf"]

tests/unit/test_config.py

@@ -4,7 +4,7 @@
 
 
 def test_config(tmp_path):
-    """Test loading the default config file."""
+    """Test loading config file."""
     os.environ["NPLINKER_ROOT_DIR"] = str(tmp_path)  # Create a temporary root dir for NPLinker
     config = load_config(CONFIG_FILE_LOCAL_MODE)
 
@@ -13,17 +13,12 @@ def test_config(tmp_path):
     assert config["log.level"] == "DEBUG"
     assert config.get("log.level") == "DEBUG"
 
-    # The following are default values from nplinker_default.toml
     assert config.get("log.file") is None
     assert config.log.use_console is True
 
     assert config.mibig.to_use is True
     assert config.mibig.version == "3.1"
 
-    assert (
-        config.bigscape.parameters
-        == "--mibig --clans-off --mix --include_singletons --cutoffs 0.30"
-    )
     assert config.bigscape.cutoff == "0.30"
     assert config.bigscape.version == 1