Causee of the error:

We imported the fairmd.lipids package, whose __init__.py raises RuntimeError when FMDL_DATA_PATH points to a non-existent folder. Develop tests shouldn't trigger that heavy package initialization, so loading the schema from the filesystem keeps them isolated.

Now loading the schema directly. If you think, loading the package initialization is necessary, you need to provide it with the proper environment in the test.

(Btw, did I mention that unconditional loading of data from an environment variblble was a bad idea?))

Author: mdondrup

tests/develop/test_autocomplete_metadata.py

@@ -1,4 +1,3 @@
-from importlib.resources import files
 import importlib.util
 import json
 import os
@@ -76,12 +75,16 @@ def test_autocomplete_output_is_schema_compliant(tmp_path, monkeypatch):
     mod.main()
 
     generated = yaml.safe_load(metadata_path.read_text(encoding="utf-8"))
-    with (
-        files("fairmd.lipids.schema_validation.schema")
-        .joinpath("metadata_schema.json")
-        .open("r", encoding="utf-8") as f
-    ):
-        schema = json.load(f)
+    schema_path = (
+        Path(__file__).resolve().parents[2]
+        / "src"
+        / "fairmd"
+        / "lipids"
+        / "schema_validation"
+        / "schema"
+        / "metadata_schema.json"
+    )
+    schema = json.loads(schema_path.read_text(encoding="utf-8"))
 
     errors = sorted(Draft7Validator(schema).iter_errors(generated), key=lambda e: e.path)
     assert not errors