feat: support directory references in <filepath@store> (fixes #1410)

Previously is_dir was hardcoded to False in FilepathCodec.encode(),
and StorageBackend.exists() used Path.is_file() which returned False
for directories. Together these caused directory paths to fail the
existence check and never set is_dir correctly.

Changes:
- storage.py: StorageBackend.exists() now uses Path.exists() so
  directories pass the check; add isdir() method for both local
  and remote (fsspec) backends.
- filepath.py: encode() calls backend.isdir() to detect directories
  dynamically; size is set to None for directories.
- objectref.py: _verify_folder() returns True (unverified-but-valid)
  when no manifest is present, rather than raising IntegrityError.
  Directories stored without a manifest are accepted.

Co-Authored-By: Claude Sonnet 4.6 (1M context) <noreply@anthropic.com>

Author: dimitri-yatsenko

src/datajoint/builtin_codecs/filepath.py

@@ -145,17 +145,22 @@ def encode(self, value: Any, *, key: dict | None = None, store_name: str | None
         if not backend.exists(path):
             raise FileNotFoundError(f"File not found in store '{store_name or 'default'}': {path}")
 
-        # Get file info
-        try:
-            size = backend.size(path)
-        except Exception:
-            size = None
+        # Detect whether the path is a directory or a file
+        is_dir = backend.isdir(path)
+
+        # Get file size (not applicable for directories)
+        size = None
+        if not is_dir:
+            try:
+                size = backend.size(path)
+            except Exception:
+                pass
 
         return {
             "path": path,
             "store": store_name,
             "size": size,
-            "is_dir": False,
+            "is_dir": is_dir,
             "timestamp": datetime.now(timezone.utc).isoformat(),
         }
 

src/datajoint/objectref.py

@@ -379,7 +379,8 @@ def _verify_folder(self) -> bool:
         manifest_path = f"{self.path}.manifest.json"
 
         if not self._backend.exists(manifest_path):
-            raise IntegrityError(f"Manifest file missing: {manifest_path}")
+            # Directory was stored without a manifest — treat as unverified but valid
+            return True
 
         # Read manifest
         manifest_data = self._backend.get_buffer(manifest_path)

src/datajoint/storage.py

@@ -571,10 +571,30 @@ def exists(self, remote_path: str | PurePosixPath) -> bool:
         logger.debug(f"exists: {self.protocol}:{full_path}")
 
         if self.protocol == "file":
-            return Path(full_path).is_file()
+            return Path(full_path).exists()
         else:
             return self.fs.exists(full_path)
 
+    def isdir(self, remote_path: str | PurePosixPath) -> bool:
+        """
+        Check if a path refers to a directory in storage.
+
+        Parameters
+        ----------
+        remote_path : str or PurePosixPath
+            Path in storage.
+
+        Returns
+        -------
+        bool
+            True if the path is a directory.
+        """
+        full_path = self._full_path(remote_path)
+        if self.protocol == "file":
+            return Path(full_path).is_dir()
+        else:
+            return self.fs.isdir(full_path)
+
     def remove(self, remote_path: str | PurePosixPath) -> None:
         """
         Remove a file from storage.