change registering to inheritance of abstract class

Registering as virtual class can avoid metclass conflicts. However, it's not an issue we need to worry in this codebase, since all concrete classes, e.g. AntismashBGCLoader,   inherit only one base class instead of multiple classes that have different metaclasses.

Using inheritance of abstract class is more straightforward and explict.

src/nplinker/genomics/antismash/antismash_loader.py

@@ -17,7 +17,7 @@
 logger = logging.getLogger(__name__)
 
 
-class AntismashBGCLoader:
+class AntismashBGCLoader(BGCLoaderBase):
     """Build a loader for AntiSMASH BGC genbank (.gbk) files.
 
     Note:
@@ -163,7 +163,3 @@ def _parse_antismash_genbank(record: SeqRecord.SeqRecord) -> dict:
                 smiles = tuple(i.replace(" ", "") for i in smiles)
             features["smiles"] = smiles
     return features
-
-
-# register as virtual class to prevent metaclass conflicts
-BGCLoaderBase.register(AntismashBGCLoader)

src/nplinker/genomics/bigscape/bigscape_loader.py

@@ -10,7 +10,7 @@
 logger = logging.getLogger(__name__)
 
 
-class BigscapeGCFLoader:
+class BigscapeGCFLoader(GCFLoaderBase):
     """Build a loader for BiG-SCAPE GCF cluster file.
 
     Attributes:
@@ -61,11 +61,7 @@ def _parse_gcf(cluster_file: str) -> list[GCF]:
         return list(gcf_dict.values())
 
 
-# register as virtual class to prevent metaclass conflicts
-GCFLoaderBase.register(BigscapeGCFLoader)
-
-
-class BigscapeV2GCFLoader:
+class BigscapeV2GCFLoader(GCFLoaderBase):
     """Build a loader for BiG-SCAPE v2 database file.
 
     Attributes:
@@ -137,7 +133,3 @@ def _parse_gcf(db_file: str) -> list[GCF]:
                 gcf_dict[family_id].bgc_ids.add(bgc_id)
 
         return list(gcf_dict.values())
-
-
-# register as virtual class to prevent metaclass conflicts
-GCFLoaderBase.register(BigscapeV2GCFLoader)

src/nplinker/genomics/mibig/mibig_loader.py

@@ -12,7 +12,7 @@
 logger = logging.getLogger(__name__)
 
 
-class MibigLoader:
+class MibigLoader(BGCLoaderBase):
     """Parse MIBiG metadata files and return BGC objects.
 
     MIBiG metadata file (json) contains annotations/metadata information
@@ -118,7 +118,3 @@ def parse_bgc_metadata_json(file: str | PathLike) -> BGC:
     mibig_bgc.mibig_bgc_class = metadata.biosyn_class
     mibig_bgc.strain = Strain(metadata.mibig_accession)
     return mibig_bgc
-
-
-# register as virtual class to prevent metaclass conflicts
-BGCLoaderBase.register(MibigLoader)