change the returned type of AntismashBGCLoader.get_bgcs

- change returned value from dict to list for `AntismashBGCLoader.get_bgcs` method and the underlying method `._parse_bgcs`
- update the use of the changed methods
- update unit tests

src/nplinker/genomics/antismash/antismash_loader.py

@@ -35,7 +35,7 @@ def __init__(self, data_dir: str) -> None:
         """
         self.data_dir = data_dir
         self._file_dict = self._parse_data_dir(self.data_dir)
-        self._bgc_dict = self._parse_bgcs(self._file_dict)
+        self._bgcs = self._parse_bgcs(self._file_dict)
 
     def get_bgc_genome_mapping(self) -> dict[str, str]:
         """Get the mapping from BGC to genome.
@@ -85,31 +85,26 @@ def _parse_data_dir(data_dir: str) -> dict[str, str]:
 
         return bgc_files
 
-    def get_bgcs(self) -> dict[str, BGC]:
+    def get_bgcs(self) -> list[BGC]:
         """Get all BGC objects.
 
         Returns:
-            dict[str, BGC]: key is BGC name and value is
-                :class:`~nplinker.genomic.BGC` objects
+            list[BGC]: a list of :class:`~nplinker.genomic.BGC` objects
         """
-        return self._bgc_dict
+        return self._bgcs
 
     @staticmethod
-    def _parse_bgcs(bgc_files: dict[str, str]) -> dict[str, BGC]:
+    def _parse_bgcs(bgc_files: dict[str, str]) -> list[BGC]:
         """Load given BGC files as BGC objects.
 
         Args:
             bgc_files(dict[str, str]): key is BGC name and value is path to the
                 BGC gbk file, see method :meth:`.bgc_files`.
 
         Returns:
-            dict[str, BGC]: key is BGC name and value is :class:`~nplinker.genomic.BGC` objects
+            list[BGC]: a list of :class:`~nplinker.genomic.BGC` objects
         """
-        bgcs = {}
-        for bgc_id in bgc_files:
-            bgc = parse_bgc_genbank(bgc_files[bgc_id])
-            bgcs[bgc_id] = bgc
-        return bgcs
+        return [parse_bgc_genbank(file) for file in bgc_files.values()]
 
 
 def parse_bgc_genbank(file: str) -> BGC:

src/nplinker/loader.py

@@ -436,8 +436,8 @@ def _load_genomics(self):
 
         # Step 1: load all BGC objects
         logger.debug("Parsing AntiSMASH directory...")
-        antismash_bgc_dict = AntismashBGCLoader(self.antismash_dir).get_bgcs()
-        raw_bgcs = list(antismash_bgc_dict.values()) + self.mibig_bgcs)
+        antismash_bgcs = AntismashBGCLoader(self.antismash_dir).get_bgcs()
+        raw_bgcs = antismash_bgcs + self.mibig_bgcs
 
         # Step 2: load all GCF objects
         bigscape_cluster_file = (

tests/genomics/antismash/test_antismash_loader.py

@@ -53,12 +53,9 @@ def test_parse_data_dir(self):
 
     def test_get_bgcs(self, loader):
         bgcs = loader.get_bgcs()
-        assert isinstance(bgcs, dict)
+        assert isinstance(bgcs, list)
         assert len(bgcs) == 44
-        assert isinstance(bgcs["NZ_AZWB01000005.region001"], BGC)
-        assert isinstance(bgcs["NZ_AZWS01000001.region001"], BGC)
-        assert bgcs.get("GCF_000514855.1", "NotExist") == "NotExist"
-        assert bgcs.get("GCF_000514515.1", "NotExist") == "NotExist"
+        assert isinstance(bgcs[0], BGC)
 
 
 def test_parse_bgc_genbank():