fix use of config for unit tests

tests/unit/__init__.py

@@ -3,3 +3,4 @@
 
 DATA_DIR = Path(__file__).resolve().parent / "data"
 GNPS_DATA_DIR = DATA_DIR / "gnps"
+CONFIG_FILE_LOCAL_MODE = DATA_DIR / "nplinker_local_mode.toml"

tests/unit/conftest.py

@@ -1,7 +1,6 @@
 import os
 import shutil
 import tempfile
-from . import DATA_DIR
 
 
 nplinker_root_dir = os.path.join(tempfile.gettempdir(), "nplinker_unit_test")
@@ -26,8 +25,6 @@ def pytest_sessionstart(session):
         os.mkdir(nplinker_root_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/unit/scoring/conftest.py

@@ -8,6 +8,7 @@
 from nplinker.scoring.linking import LinkFinder
 from nplinker.strain import Strain
 from nplinker.strain import StrainCollection
+from .. import CONFIG_FILE_LOCAL_MODE
 
 
 @fixture(scope="session")
@@ -86,7 +87,7 @@ def npl(gcfs, spectra, mfs, strains, tmp_path_factory) -> NPLinker:
     The config file `nplinker_demo1.toml` does not affect the tests, just
     making sure the NPLinker object can be created succesfully.
     """
-    npl = NPLinker()
+    npl = NPLinker(CONFIG_FILE_LOCAL_MODE)
     npl._gcfs = gcfs
     npl._spectra = spectra
     npl._molfams = mfs

tests/unit/test_config.py

@@ -1,9 +1,11 @@
-from nplinker.config import config
+from nplinker.config import load_config
+from . import CONFIG_FILE_LOCAL_MODE
 
 
 def test_config():
     """Test loading the default config file."""
-    # The default config file is set in "./conftest.py", which is "data/nplinker_local_mode.toml"
+    config = load_config(CONFIG_FILE_LOCAL_MODE)
+
     assert config.mode == "local"
     assert config.log.level == "DEBUG"
     assert config["log.level"] == "DEBUG"