fix skipping relativize absolute paths that are first-level root directories

src/numpydantic/serialization.py

@@ -64,14 +64,20 @@ def _relativize_paths(
     ``relative_to`` directory, if provided in the context
     """
     relative_to = Path(relative_to).resolve()
-    # pdb.set_trace()
 
     def _r_path(v: Any) -> Any:
         if not isinstance(v, (str, Path)):
             return v
         try:
             path = Path(v)
-            if not path.exists():
+            resolved = path.resolve()
+            # skip things that are pathlike but either don't exist
+            # or that are at the filesystem root (eg like /data)
+            if (
+                not path.exists()
+                or (resolved.is_dir() and str(resolved.parent) == resolved.root)
+                or relative_to.root != resolved.root
+            ):
                 return v
             return str(relative_path(path, relative_to))
         except (TypeError, ValueError):
@@ -86,9 +92,7 @@ def _absolutize_paths(value: dict, skip: Iterable = tuple()) -> dict:
             return v
         try:
             path = Path(v)
-            # skip things that are pathlike but either don't exist
+            if not path.exists():
-            # or that are at the filesystem root (eg like /data)
-            if not path.exists() and path.parent != Path().root:
                 return v
             return str(path.resolve())
         except (TypeError, ValueError):

tests/test_serialization.py

@@ -10,7 +10,7 @@ from typing import Callable
 import numpy as np
 import json
 
-from numpydantic.serialization import _walk_and_apply
+from numpydantic.serialization import _walk_and_apply, _relativize_paths, relative_path
 
 pytestmark = pytest.mark.serialization
 
@@ -56,7 +56,7 @@ def test_relative_to_path(hdf5_at_path, tmp_output_dir, model_blank):
     """
     out_path = tmp_output_dir / "relative.h5"
     relative_to_path = Path(__file__) / "fake_dir" / "sub_fake_dir"
-    expected_path = "../../../__tmp__/relative.h5"
+    expected_path = Path("../../../__tmp__/relative.h5")
 
     hdf5_at_path(out_path)
     model = model_blank(array=(out_path, "/data"))
@@ -69,13 +69,34 @@ def test_relative_to_path(hdf5_at_path, tmp_output_dir, model_blank):
     # should not be absolute
     assert not Path(file).is_absolute()
     # should be expected path and reach the file
-    assert file == expected_path
+    assert Path(file) == expected_path
     assert (relative_to_path / file).resolve() == out_path.resolve()
 
     # we shouldn't have touched `/data` even though it is pathlike
     assert data["path"] == "/data"
 
 
+def test_relative_to_root_dir():
+    """
+    The relativize function should ignore paths that are directories
+    beneath the root directory (eg `/data`) even if they exist
+
+    """
+    root = Path().resolve().parents[-1]
+    test_path = None
+    for path in root.iterdir():
+        if path.is_dir():
+            test_path = path
+
+    assert test_path is not None
+
+    test_data = {"some_field": str(test_path)}
+
+    walked = _relativize_paths(test_data, relative_to=".")
+    assert str(relative_path(test_path, Path(".").resolve())) != str(test_path)
+    assert walked["some_field"] == str(test_path)
+
+
 def test_absolute_path(hdf5_at_path, tmp_output_dir, model_blank):
     """
     When told, we make paths absolute