update tests

lindi/LindiH5pyFile/LindiH5pyDataset.py

@@ -78,11 +78,13 @@ def _resolve_references(x: Any):
         else:
             for k, v in x.items():
                 x[k] = _resolve_references(v)
+    elif isinstance(x, LindiZarrWrapperReference):
+        return LindiH5pyReference(x)
     elif isinstance(x, list):
         for i, v in enumerate(x):
             x[i] = _resolve_references(v)
     elif isinstance(x, np.ndarray):
-        if x.dtype == object:
+        if x.dtype == object or x.dtype is None:
             view_1d = x.reshape(-1)
             for i in range(len(view_1d)):
                 view_1d[i] = _resolve_references(view_1d[i])

lindi/LindiH5pyFile/LindiH5pyFile.py

@@ -4,7 +4,7 @@
 
 from .LindiH5pyGroup import LindiH5pyGroup
 from .LindiH5pyDataset import LindiH5pyDataset
-from ..LindiZarrWrapper import LindiZarrWrapper, LindiZarrWrapperGroup, LindiZarrWrapperDataset
+from ..LindiZarrWrapper import LindiZarrWrapper, LindiZarrWrapperGroup, LindiZarrWrapperDataset, LindiZarrWrapperReference
 from .LindiH5pyAttributes import LindiH5pyAttributes
 from .LindiH5pyReference import LindiH5pyReference
 
@@ -99,6 +99,10 @@ def __repr__(self):
     # Group methods
 
     def __getitem__(self, name):
+        if isinstance(name, LindiZarrWrapperReference):
+            # annoyingly we have to do this because references
+            # in arrays of compound types will come in as LindiZarrWrapperReference
+            name = LindiH5pyReference(name)
         if isinstance(name, LindiH5pyReference):
             assert isinstance(self._file_object, LindiZarrWrapper)
             x = self._file_object[name._reference]
@@ -117,6 +121,13 @@ def __getitem__(self, name):
                 return LindiH5pyDataset(x, self)
             else:
                 raise Exception(f"Unexpected type for resolved reference at path {name}: {type(x)}")
+        # if it contains slashes, it's a path
+        if isinstance(name, str) and "/" in name:
+            parts = name.split("/")
+            x = self._the_group
+            for part in parts:
+                x = x[part]
+            return x
         return self._the_group[name]
 
     def get(self, name, default=None, getclass=False, getlink=False):

lindi/LindiH5pyFile/LindiH5pyLink.py

@@ -1,9 +1,12 @@
-class LindiH5pyHardLink:
+import h5py
+
+
+class LindiH5pyHardLink(h5py.HardLink):
     def __init__(self):
         pass
 
 
-class LindiH5pySoftLink:
+class LindiH5pySoftLink(h5py.SoftLink):
     def __init__(self, path: str):
         self._path = path
 

lindi/LindiZarrWrapper/LindiZarrWrapperReference.py

@@ -1,4 +1,9 @@
-class LindiZarrWrapperReference:
+import h5py
+
+
+# We need h5py.Reference as a base class so that type checking will be okay for
+# arrays of compound types that contain references
+class LindiZarrWrapperReference(h5py.Reference):
     def __init__(self, obj: dict):
         self._object_id = obj["object_id"]
         self._path = obj["path"]