update the use of the new ScoringBase class

src/nplinker/nplinker.py

@@ -15,9 +15,9 @@
 from .metabolomics import MolecularFamily
 from .metabolomics import Spectrum
 from .pickler import save_pickled_data
+from .scoring.abc import ScoringBase
 from .scoring.link_collection import LinkCollection
 from .scoring.metcalf_scoring import MetcalfScoring
-from .scoring.methods import ScoringMethod
 from .scoring.np_class_scoring import NPClassScoring
 from .scoring.rosetta_scoring import RosettaScoring
 
@@ -37,9 +37,9 @@ class NPLinker:
     # default set of enabled scoring methods
     # TODO: ideally these shouldn't be hardcoded like this
     SCORING_METHODS = {
-        MetcalfScoring.NAME: MetcalfScoring,
-        RosettaScoring.NAME: RosettaScoring,
-        NPClassScoring.NAME: NPClassScoring,
+        MetcalfScoring.name: MetcalfScoring,
+        RosettaScoring.name: RosettaScoring,
+        NPClassScoring.name: NPClassScoring,
     }
 
     def __init__(self, config_file: str | PathLike):
@@ -266,7 +266,7 @@ def get_links(
 
         if not self._datalinks:
             logger.debug("Creating internal datalinks object")
-            self._datalinks = self.scoring_method(MetcalfScoring.NAME).datalinks
+            self._datalinks = self.scoring_method(MetcalfScoring.name).datalinks
             logger.debug("Created internal datalinks object")
 
         if len(link_collection) == 0:
@@ -318,7 +318,7 @@ def get_common_strains(
             and values are a list of shared Strain objects.
         """
         if not self._datalinks:
-            self._datalinks = self.scoring_method(MetcalfScoring.NAME).datalinks
+            self._datalinks = self.scoring_method(MetcalfScoring.name).datalinks
         common_strains = self._datalinks.get_common_strains(met, gcfs, filter_no_shared)
         return common_strains
 
@@ -401,7 +401,7 @@ def class_matches(self):
         """ClassMatches with the matched classes and scoring tables from MIBiG."""
         return self._class_matches
 
-    def scoring_method(self, name: str) -> ScoringMethod | None:
+    def scoring_method(self, name: str) -> ScoringBase | None:
         """Return an instance of a scoring method.
 
         Args:

src/nplinker/scoring/metcalf_scoring.py

@@ -9,11 +9,11 @@
 from nplinker.metabolomics import Spectrum
 from nplinker.pickler import load_pickled_data
 from nplinker.pickler import save_pickled_data
+from .abc import ScoringBase
 from .linking import LINK_TYPES
 from .linking import DataLinks
 from .linking import LinkFinder
 from .linking import isinstance_all
-from .methods import ScoringMethod
 from .object_link import ObjectLink
 
 
@@ -24,19 +24,19 @@
 logger = logging.getLogger(__name__)
 
 
-class MetcalfScoring(ScoringMethod):
+class MetcalfScoring(ScoringBase):
     """Metcalf scoring method.
 
     Attributes:
+        name: The name of this scoring method, set to a fixed value `metcalf`.
         DATALINKS: The DataLinks object to use for scoring.
         LINKFINDER: The LinkFinder object to use for scoring.
-        NAME: The name of the scoring method. This is set to 'metcalf'.
         CACHE: The name of the cache file to use for storing the MetcalfScoring.
     """
 
+    name = "metcalf"
     DATALINKS = None
     LINKFINDER = None
-    NAME = "metcalf"
     CACHE = "cache_metcalf_scoring.pckl"
 
     def __init__(self, npl: NPLinker) -> None:

src/nplinker/scoring/np_class_scoring.py

@@ -3,16 +3,16 @@
 from nplinker.genomics import BGC
 from nplinker.genomics import GCF
 from nplinker.metabolomics import Spectrum
+from nplinker.scoring.abc import ScoringBase
 from nplinker.scoring.metcalf_scoring import MetcalfScoring
-from nplinker.scoring.methods import ScoringMethod
 from nplinker.scoring.object_link import ObjectLink
 
 
 logger = logging.getLogger(__name__)
 
 
-class NPClassScoring(ScoringMethod):
-    NAME = "npclassscore"
+class NPClassScoring(ScoringBase):
+    name = "npclassscore"
 
     def __init__(self, npl):
         super().__init__(npl)
@@ -347,7 +347,7 @@ def get_links(self, objects, link_collection):
         logger.info("Using Metcalf scoring to get shared strains")
         # get mapping of shared strains
         if not self.npl._datalinks:
-            self.npl._datalinks = self.npl.scoring_method(MetcalfScoring.NAME).datalinks
+            self.npl._datalinks = self.npl.scoring_method(MetcalfScoring.name).datalinks
         if obj_is_gen:
             common_strains = self.npl.get_common_strains(targets, objects)
         else:

src/nplinker/scoring/rosetta_scoring.py

@@ -3,16 +3,16 @@
 from nplinker.genomics.bgc import BGC
 from nplinker.genomics.gcf import GCF
 from nplinker.metabolomics import MolecularFamily
-from nplinker.scoring.methods import ScoringMethod
+from nplinker.scoring.abc import ScoringBase
 from nplinker.scoring.object_link import ObjectLink
 from nplinker.scoring.rosetta.rosetta import Rosetta
 
 
 logger = logging.getLogger(__name__)
 
 
-class RosettaScoring(ScoringMethod):
-    NAME = "rosetta"
+class RosettaScoring(ScoringBase):
+    name = "rosetta"
     ROSETTA_OBJ = None
 
     def __init__(self, npl):