fix use of config for integration tests

src/nplinker/arranger.py

@@ -263,15 +263,15 @@ def arrange_bigscape(self) -> None:
         if self.config.mode == "podp":
             for _ in range(3):
                 try:
-                    validate_bigscape(self.bigscape_dir)
+                    validate_bigscape(self.bigscape_dir, self.config.bigscape.cutoff)
                     pass_validation = True
                     break
                 except FileNotFoundError:
                     shutil.rmtree(self.bigscape_dir, ignore_errors=True)
                     self._run_bigscape()
 
         if not pass_validation:
-            validate_bigscape(self.bigscape_dir)
+            validate_bigscape(self.bigscape_dir, self.config.bigscape.cutoff)
 
     def _run_bigscape(self) -> None:
         """Run BiG-SCAPE to generate the clustering file.
@@ -460,7 +460,7 @@ def validate_antismash(antismash_dir: Path) -> None:
             raise FileNotFoundError(f"No BGC files found in antiSMASH sub-directory {sub_dir}")
 
 
-def validate_bigscape(bigscape_dir: Path) -> None:
+def validate_bigscape(bigscape_dir: Path, cutoff: str) -> None:
     """Validate the BiG-SCAPE data directory and its contents.
 
     The BiG-SCAPE data directory must exist and contain the clustering file
@@ -473,14 +473,15 @@ def validate_bigscape(bigscape_dir: Path) -> None:
 
     Args:
         bigscape_dir: Path to the BiG-SCAPE data directory.
+        cutoff: The BiG-SCAPE cutoff value.
 
     Raises:
         FileNotFoundError: If the BiG-SCAPE data directory or the clustering file is not found.
     """
     if not bigscape_dir.exists():
         raise FileNotFoundError(f"BiG-SCAPE data directory not found at {bigscape_dir}")
 
-    clustering_file = bigscape_dir / f"mix_clustering_c{self.config.bigscape.cutoff}.tsv"
+    clustering_file = bigscape_dir / f"mix_clustering_c{cutoff}.tsv"
     database_file = bigscape_dir / "data_sqlite.db"
     if not clustering_file.exists() and not database_file.exists():
         raise FileNotFoundError(f"BiG-SCAPE data not found in {clustering_file} or {database_file}")

tests/integration/conftest.py

@@ -46,8 +46,6 @@ def pytest_sessionstart(session):
             zip_ref.extractall(temp_dir)
     # NPLinker setting `root_dir` must be a path that exists, so setting it to a temporary directory.
     os.environ["NPLINKER_ROOT_DIR"] = nplinker_root_dir
-    # # Specify the config file via environment variable before importing nplinker in any test.
-    os.environ["NPLINKER_CONFIG_FILE"] = str(DATA_DIR / "nplinker_local_mode.toml")
 
 
 def pytest_sessionfinish(session):

tests/integration/test_nplinker_local.py

@@ -2,6 +2,7 @@
 from pathlib import Path
 import pytest
 from nplinker.nplinker import NPLinker
+from . import DATA_DIR
 
 
 # Only tests related to data arranging and loading should be put here.
@@ -23,7 +24,7 @@ def get_file_hash(file_path):
 
 @pytest.fixture(scope="module")
 def npl() -> NPLinker:
-    npl = NPLinker()
+    npl = NPLinker(DATA_DIR / "nplinker_local_mode.toml")
     npl.load_data()
     # remove cached score results before running tests
     root_dir = Path(npl.root_dir)