Merge branch 'master' into enh-lad-docstrings-core

Author: CodyCBakerPhD

CHANGELOG.md

@@ -1,3 +1,23 @@
+# 0.74.3 (Sat Feb 14 2026)
+
+#### 🐛 Bug Fix
+
+- bf: pass aiohttp timeouts to fsspec to fix test hang [#1795](https://github.com/dandi/dandi-cli/pull/1795) ([@yarikoptic](https://github.com/yarikoptic))
+- Enhance dandiset metadata error messages [#1790](https://github.com/dandi/dandi-cli/pull/1790) ([@yarikoptic](https://github.com/yarikoptic) [@yarikoptic-gitmate](https://github.com/yarikoptic-gitmate))
+- Fix type annotation in upload sync path prefix calculation [#1794](https://github.com/dandi/dandi-cli/pull/1794) ([@yarikoptic](https://github.com/yarikoptic) [@yarikoptic-gitmate](https://github.com/yarikoptic-gitmate))
+- Fix macOS-15-intel CI failures: h5py and opencv-python regressions [#1783](https://github.com/dandi/dandi-cli/pull/1783) ([@yarikoptic](https://github.com/yarikoptic))
+
+#### 📝 Documentation
+
+- Add module docstrings to validation and NWB utilities [#1789](https://github.com/dandi/dandi-cli/pull/1789) ([@yarikoptic](https://github.com/yarikoptic) [@yarikoptic-gitmate](https://github.com/yarikoptic-gitmate))
+
+#### Authors: 2
+
+- GitMate for @yarikoptic ([@yarikoptic-gitmate](https://github.com/yarikoptic-gitmate))
+- Yaroslav Halchenko ([@yarikoptic](https://github.com/yarikoptic))
+
+---
+
 # 0.74.2 (Fri Jan 30 2026)
 
 #### 🐛 Bug Fix

dandi/dandiset.py

@@ -42,7 +42,11 @@ def __init__(
         if not allow_empty and not os.path.lexists(
             self.path_obj / dandiset_metadata_file
         ):
-            raise ValueError(f"No dandiset at {path}")
+            raise ValueError(
+                f"No dandiset at {path}. "
+                f"The directory does not contain a '{dandiset_metadata_file}' file. "
+                "Use 'dandi download' to download a dandiset or check the path."
+            )
         self.metadata: dict | None = None
         self._metadata_file_obj = self.path_obj / dandiset_metadata_file
         self._load_metadata()
@@ -139,11 +143,17 @@ def _get_identifier(metadata: dict) -> str | None:
     @property
     def identifier(self) -> str:
         if self.metadata is None:
-            raise ValueError("No metadata record found in Dandiset")
+            raise ValueError(
+                f"No metadata record found in Dandiset at {self.path}. "
+                f"The '{dandiset_metadata_file}' file may be empty or corrupted. "
+                "Use 'dandi download' to re-download the dandiset metadata."
+            )
         id_ = self._get_identifier(self.metadata)
         if not id_:
             raise ValueError(
-                f"Found no dandiset.identifier in metadata record: {self.metadata}"
+                f"Found no dandiset.identifier in metadata record. "
+                f"The '{dandiset_metadata_file}' file must contain an 'identifier' field. "
+                f"Metadata: {self.metadata}"
             )
         return id_
 

dandi/delete.py

@@ -1,3 +1,13 @@
+"""Delete assets and dandisets from DANDI Archive.
+
+This module provides functionality for deleting assets and entire dandisets
+from DANDI Archive instances. It supports:
+- Single and batch asset deletion
+- Dandiset deletion with confirmation
+- URL-based and path-based deletion
+- Skip-missing option for non-existent resources
+"""
+
 from __future__ import annotations
 
 from collections.abc import Iterable, Iterator

dandi/download.py

@@ -1,3 +1,13 @@
+"""Download assets from DANDI Archive.
+
+This module provides functionality for downloading files and Zarr archives
+from DANDI Archive instances. It supports:
+- Individual file downloads with integrity verification
+- Zarr archive downloads with parallel entry handling
+- Resume capability for interrupted downloads
+- Progress tracking and error recovery
+"""
+
 from __future__ import annotations
 
 from collections import Counter, deque

dandi/misctypes.py

@@ -345,10 +345,27 @@ def open(self) -> IO[bytes]:
         # Optional dependency:
         import fsspec
 
+        from aiohttp import ClientTimeout
+
         # We need to call open() on the return value of fsspec.open() because
         # otherwise the filehandle will only be opened when used to enter a
         # context manager.
-        return cast(IO[bytes], fsspec.open(self.url, mode="rb").open())
+        #
+        # Pass explicit timeouts to aiohttp to prevent indefinite hangs in
+        # fsspec's sync() wrapper.  Without these, a stalled connection to S3
+        # (or minio in tests) causes fsspec's background IO thread to block
+        # forever, which in turn blocks the calling thread in
+        # threading.Event.wait() — see https://github.com/fsspec/filesystem_spec/issues/1666
+        return cast(
+            IO[bytes],
+            fsspec.open(
+                self.url,
+                mode="rb",
+                client_kwargs={
+                    "timeout": ClientTimeout(total=120, sock_read=60, sock_connect=30)
+                },
+            ).open(),
+        )
 
     def get_size(self) -> int:
         return self.size

dandi/move.py

@@ -1,3 +1,14 @@
+"""Move and rename assets in DANDI Archive.
+
+This module provides functionality for moving and renaming assets both
+locally and remotely in DANDI Archive instances. Features include:
+- Local file reorganization
+- Remote asset path changes
+- Combined local and remote moves
+- Conflict resolution (skip, overwrite, error)
+- Validation of move operations
+"""
+
 from __future__ import annotations
 
 from abc import ABC, abstractmethod

dandi/organize.py

@@ -1,5 +1,12 @@
-"""
-ATM primarily a sandbox for some functionality for dandi organize
+"""Organize and structure NWB files according to DANDI conventions.
+
+This module provides functionality for organizing neuroscience data files
+according to DANDI's file organization schema. Features include:
+- Automatic path generation from metadata
+- BIDS-like subject/session organization
+- Metadata-driven file naming
+- Validation of organized paths
+- Support for videos and generic files
 """
 
 from __future__ import annotations

dandi/pynwb_utils.py

@@ -1,3 +1,14 @@
+"""Utilities for working with NWB (Neurodata Without Borders) files.
+
+This module provides helper functions for reading, validating, and extracting
+metadata from NWB files using PyNWB. Features include:
+- NWB file I/O with caching
+- Metadata extraction for DANDI schema
+- Version compatibility checking
+- External link detection
+- Validation against NWB standards
+"""
+
 from __future__ import annotations
 
 from collections import Counter

dandi/tests/test_metadata.py

@@ -1145,6 +1145,7 @@ def test_nwb2asset(simple2_nwb: Path) -> None:
     )
 
 
+@pytest.mark.timeout(120)
 @pytest.mark.xfail(reason="https://github.com/dandi/dandi-cli/issues/1450")
 def test_nwb2asset_remote_asset(nwb_dandiset: SampleDandiset) -> None:
     pytest.importorskip("fsspec")

dandi/upload.py

@@ -1,10 +1,20 @@
+"""Upload assets to DANDI Archive.
+
+This module handles uploading NWB files and other assets to DANDI Archive
+instances. Features include:
+- Validation of files before upload
+- Progress tracking with resume capability
+- Metadata extraction and assignment
+- BIDS validation integration
+- Concurrent uploads with thread pool
+"""
+
 from __future__ import annotations
 
 from collections import defaultdict
 from collections.abc import Iterator, Sequence
 from contextlib import ExitStack
 from enum import Enum
-from functools import reduce
 import io
 import os.path
 from pathlib import Path
@@ -493,7 +503,7 @@ def upload_agg(*ignored: Any) -> str:
             for p in paths:
                 rp = os.path.relpath(p, dandiset.path)
                 relpaths.append("" if rp == "." else rp)
-            path_prefix = reduce(os.path.commonprefix, relpaths)  # type: ignore[arg-type]
+            path_prefix = os.path.commonprefix(relpaths)
             to_delete = []
             for asset in remote_dandiset.get_assets_with_path_prefix(path_prefix):
                 if any(