fix case if input is 'optimade.jsonl'

examples/direct_from_jsonl/optimade.yaml

@@ -4,4 +4,4 @@ database_description: >-
   This database contains some example CIFs.
 
 entries:
-  jsonl_path: example.jsonl
+  jsonl_path: optimade.jsonl

src/optimake/convert.py

@@ -80,7 +80,12 @@ def convert_archive(archive_path: Path, jsonl_path: Path | None = None) -> Path:
     if isinstance(mc_config.entries, JSONLConfig):
         if mc_config.entries.file is not None:
             inflate_archive(archive_path, Path(mc_config.entries.file))
-        jsonl_path.symlink_to(archive_path / mc_config.entries.jsonl_path)
+        src_jsonl_path = archive_path / mc_config.entries.jsonl_path
+        if jsonl_path != src_jsonl_path:
+            # add a symlink to the specified jsonl_path
+            if jsonl_path.exists():
+                raise RuntimeError(f"Not overwriting existing file at {jsonl_path}")
+            jsonl_path.symlink_to(archive_path / src_jsonl_path)
         return jsonl_path
 
     # first, decompress any provided data paths

tests/test_convert.py

@@ -23,9 +23,6 @@ def test_convert_example_archives(archive_path, tmp_path):
     tmp_path = tmp_path / archive_path.name
     shutil.copytree(archive_path, tmp_path)
 
-    # remove 'optimade.jsonl' if the example was already run
-    (tmp_path / "optimade.jsonl").unlink(missing_ok=True)
-
     jsonl_path = convert_archive(tmp_path)
     assert jsonl_path.exists()