Merge pull request #177 from NPLinker/update_ruff_rules

Update ruff rules to ignore unused imports in `__init__.py` files

pyproject.toml

@@ -96,6 +96,8 @@ ignore = [
 
 # Allow autofix for all enabled rules (when `--fix`) is provided.
 fixable = ["A", "B", "C", "D", "E", "F", "I"]
+ignore-init-module-imports = true
+
 
 [tool.ruff.isort]
 known-first-party = ["nplinker"]

src/nplinker/genomics/mibig/__init__.py

@@ -1,4 +1,15 @@
 import logging
+from .mibig_downloader import download_and_extract_mibig_metadata
+from .mibig_loader import MibigLoader
+from .mibig_loader import parse_bgc_metadata_json
+from .mibig_metadata import MibigMetadata
 
 
 logging.getLogger(__name__).addHandler(logging.NullHandler())
+
+__all__ = [
+    "download_and_extract_mibig_metadata",
+    "MibigLoader",
+    "MibigMetadata",
+    "parse_bgc_metadata_json",
+]

tests/genomics/test_bigscape_loader.py

@@ -34,12 +34,8 @@ def test_get_gcfs_without_mibig_only(self, loader):
         assert isinstance(gcfs[0], GCF)
 
     def test_parse_gcf(self, loader):
-        gcf_dict = BigscapeGCFLoader._parse_gcf(loader.cluster_file)  # noqa
-        assert isinstance(gcf_dict, dict)
-        assert len(gcf_dict) == 114
-        gcf = gcf_dict["135"]
-        assert isinstance(gcf, GCF)
-        assert len(gcf.bgc_ids) == 4
-        assert gcf.bgc_ids == set(
-            ("BGC0000145", "BGC0001041", "NC_009380.1.region004", "NZ_AZWK01000002.region002")
-        )
+        gcf_list = BigscapeGCFLoader._parse_gcf(loader.cluster_file)  # noqa
+        assert isinstance(gcf_list, list)
+        assert len(gcf_list) == 114
+        for gcf in gcf_list:
+            assert isinstance(gcf, GCF)