Dandi

🚀 Enhancement

- enh: add cellline parsing [1254](https://github.com/dandi/dandi-cli/pull/1254) ([satra](https://github.com/satra) [yarikoptic](https://github.com/yarikoptic))
- [ENH] Add severity restriction option to `dandi-validate` [1248](https://github.com/dandi/dandi-cli/pull/1248) ([TheChymera](https://github.com/TheChymera))

🐛 Bug Fix

- Log more information about retried HTTP requests [1264](https://github.com/dandi/dandi-cli/pull/1264) ([jwodder](https://github.com/jwodder))

📝 Documentation

- Add an example for streaming using as_readable + reference to PyNWB examples [1250](https://github.com/dandi/dandi-cli/pull/1250) ([yarikoptic](https://github.com/yarikoptic))

🧪 Tests

- Add CI run testing against NFS [1262](https://github.com/dandi/dandi-cli/pull/1262) ([jwodder](https://github.com/jwodder))
- Creating test for file-wise NWB error output listing [1244](https://github.com/dandi/dandi-cli/pull/1244) ([TheChymera](https://github.com/TheChymera))

Authors: 4

- Horea Christian ([TheChymera](https://github.com/TheChymera))
- John T. Wodder II ([jwodder](https://github.com/jwodder))
- Satrajit Ghosh ([satra](https://github.com/satra))
- Yaroslav Halchenko ([yarikoptic](https://github.com/yarikoptic))

---

🚀 Enhancement

- `validate`: Yield error if path is not inside a Dandiset [1237](https://github.com/dandi/dandi-cli/pull/1237) ([jwodder](https://github.com/jwodder))
- Add service script for re-extracting remote NWB metadata [1236](https://github.com/dandi/dandi-cli/pull/1236) ([jwodder](https://github.com/jwodder))

📝 Documentation

- Corrected docstring [1245](https://github.com/dandi/dandi-cli/pull/1245) ([TheChymera](https://github.com/TheChymera))

🧪 Tests

- Revert "Restrict mypy to pre-v1.1.1" [1247](https://github.com/dandi/dandi-cli/pull/1247) ([jwodder](https://github.com/jwodder))
- Restrict mypy to pre-v1.1.1 [1246](https://github.com/dandi/dandi-cli/pull/1246) ([jwodder](https://github.com/jwodder))
- Skip reextract-metadata test if fsspec is not installed [1240](https://github.com/dandi/dandi-cli/pull/1240) ([jwodder](https://github.com/jwodder))

🔩 Dependency Updates

- Update for dandischema 0.8.0 [1241](https://github.com/dandi/dandi-cli/pull/1241) ([jwodder](https://github.com/jwodder) [yarikoptic](https://github.com/yarikoptic))

Authors: 3

- Horea Christian ([TheChymera](https://github.com/TheChymera))
- John T. Wodder II ([jwodder](https://github.com/jwodder))
- Yaroslav Halchenko ([yarikoptic](https://github.com/yarikoptic))

---

🧪 Tests

- skip test_nwb2asset_remote_asset if no fsspec installed [1239](https://github.com/dandi/dandi-cli/pull/1239) ([yarikoptic](https://github.com/yarikoptic))

Authors: 1

- Yaroslav Halchenko ([yarikoptic](https://github.com/yarikoptic))

---

🚀 Enhancement

- Add `--ignore ID_REGEX` option to `dandi validate` [1234](https://github.com/dandi/dandi-cli/pull/1234) ([jwodder](https://github.com/jwodder))
- download: support for downloading multiple URLs at once; dandiset path is now included in the report [1231](https://github.com/dandi/dandi-cli/pull/1231) ([jwodder](https://github.com/jwodder))
- Merging `bids_validate` into `validate`, stop validating nested BIDS. [1203](https://github.com/dandi/dandi-cli/pull/1203) ([TheChymera](https://github.com/TheChymera) [jwodder](https://github.com/jwodder))
- Support re-extracting metadata from remote assets [1214](https://github.com/dandi/dandi-cli/pull/1214) ([jwodder](https://github.com/jwodder))

🐛 Bug Fix

- Inform user with a warning in case of jobs > 1 but non pyout format [1222](https://github.com/dandi/dandi-cli/pull/1222) ([yarikoptic](https://github.com/yarikoptic))
- BF: add missing f- for a string [1228](https://github.com/dandi/dandi-cli/pull/1228) ([yarikoptic](https://github.com/yarikoptic))
- Don't even test for `cp --reflink` support on Windows [1221](https://github.com/dandi/dandi-cli/pull/1221) ([jwodder](https://github.com/jwodder))
- Filter out pyout logs from logfile by default [1220](https://github.com/dandi/dandi-cli/pull/1220) ([jwodder](https://github.com/jwodder))
- Metadata: add extraction of strain from nwb files [1216](https://github.com/dandi/dandi-cli/pull/1216) ([satra](https://github.com/satra) [yarikoptic](https://github.com/yarikoptic))

🏠 Internal

- Use pathlib more in tests [1233](https://github.com/dandi/dandi-cli/pull/1233) ([jwodder](https://github.com/jwodder))

📝 Documentation

- Added distribution badge (sadly only one ATM) [1224](https://github.com/dandi/dandi-cli/pull/1224) ([TheChymera](https://github.com/TheChymera))
- List in documentation the "high level" interfaces corresponding to CLI [1200](https://github.com/dandi/dandi-cli/pull/1200) ([yarikoptic](https://github.com/yarikoptic))

🧪 Tests

- Update `parse_purlobourl()` test for change to rat metadata [1227](https://github.com/dandi/dandi-cli/pull/1227) ([jwodder](https://github.com/jwodder))
- Revert "Temporarily disable all tests which talk to obolibrary" - ontobee said to be back [1226](https://github.com/dandi/dandi-cli/pull/1226) ([yarikoptic](https://github.com/yarikoptic))
- Fix tests: avoid obolibrary (for now) and pynwb 2.3.0 (forever) [1225](https://github.com/dandi/dandi-cli/pull/1225) ([yarikoptic](https://github.com/yarikoptic))
- Test against Python 3.11 [1143](https://github.com/dandi/dandi-cli/pull/1143) ([jwodder](https://github.com/jwodder))

Authors: 4

- Horea Christian ([TheChymera](https://github.com/TheChymera))
- John T. Wodder II ([jwodder](https://github.com/jwodder))
- Satrajit Ghosh ([satra](https://github.com/satra))
- Yaroslav Halchenko ([yarikoptic](https://github.com/yarikoptic))

---

🐛 Bug Fix

- Update for fix to Zarr upload procedure [1215](https://github.com/dandi/dandi-cli/pull/1215) ([jwodder](https://github.com/jwodder))

🧪 Tests

- Restore testing against Windows with Python 3.10 [1213](https://github.com/dandi/dandi-cli/pull/1213) ([jwodder](https://github.com/jwodder))

Authors: 1

- John T. Wodder II ([jwodder](https://github.com/jwodder))

---

🚀 Enhancement

- Update for new Zarr upload procedure; remove no longer needed `service-scripts` [1202](https://github.com/dandi/dandi-cli/pull/1202) ([jwodder](https://github.com/jwodder))
- BF+RF validation [1209](https://github.com/dandi/dandi-cli/pull/1209) ([yarikoptic](https://github.com/yarikoptic))

🐛 Bug Fix

- Make `RemoteDandiset.get_version()` return a `VersionInfo` instance with validation error fields [1210](https://github.com/dandi/dandi-cli/pull/1210) ([jwodder](https://github.com/jwodder))
- Improve messages displayed when an upload fails [1204](https://github.com/dandi/dandi-cli/pull/1204) ([jwodder](https://github.com/jwodder))
- RF/BF: make find_parent_directory_containing operate on absolute path [1188](https://github.com/dandi/dandi-cli/pull/1188) ([yarikoptic](https://github.com/yarikoptic))

🏠 Internal

- Pass $USER to tox envs [1201](https://github.com/dandi/dandi-cli/pull/1201) ([jwodder](https://github.com/jwodder))
- boost isort in precommit to 5.12.0 to overcome issue with poetry [1199](https://github.com/dandi/dandi-cli/pull/1199) ([yarikoptic](https://github.com/yarikoptic))

📝 Documentation

- Move doc/design under docs/ where the rest of docs reside [1198](https://github.com/dandi/dandi-cli/pull/1198) ([yarikoptic](https://github.com/yarikoptic))
- Further improve README.md: point to specific sections of handbook, remove lengthy `dandi ls --help` example [1193](https://github.com/dandi/dandi-cli/pull/1193) ([melster1010](https://github.com/melster1010))

🧪 Tests

- Fix type errors; unbound mypy [1207](https://github.com/dandi/dandi-cli/pull/1207) ([jwodder](https://github.com/jwodder))
- We no longer need to catch warning as hdmf has fixed the bug [1194](https://github.com/dandi/dandi-cli/pull/1194) ([TheChymera](https://github.com/TheChymera))
- Joint BIDS-NWB metadata extraction. [1183](https://github.com/dandi/dandi-cli/pull/1183) ([TheChymera](https://github.com/TheChymera))
- Fix for newer HDMF [1191](https://github.com/dandi/dandi-cli/pull/1191) ([TheChymera](https://github.com/TheChymera))

🔩 Dependency Updates

- Blacklisting the most recent hdmf version 3.5.0 forbidding its use and breaking CI/testing. [1190](https://github.com/dandi/dandi-cli/pull/1190) ([TheChymera](https://github.com/TheChymera))

Authors: 4

- Horea Christian ([TheChymera](https://github.com/TheChymera))
- John T. Wodder II ([jwodder](https://github.com/jwodder))
- Mary Elise Dedicke ([melster1010](https://github.com/melster1010))
- Yaroslav Halchenko ([yarikoptic](https://github.com/yarikoptic))

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