Dandi

🐛 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))

---

🐛 Bug Fix

- Fail upload only for validation ERRORs and not necessarily WARNINGs or HINTs + log all errors [1186](https://github.com/dandi/dandi-cli/pull/1186) ([yarikoptic](https://github.com/yarikoptic))
- Don't warn on unexpected formats for "next" page URLs [1184](https://github.com/dandi/dandi-cli/pull/1184) ([jwodder](https://github.com/jwodder))
- Upload test to check for metadata [1180](https://github.com/dandi/dandi-cli/pull/1180) ([TheChymera](https://github.com/TheChymera))

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))

---

🚀 Enhancement

- Update client for change in Zarr entries API [1175](https://github.com/dandi/dandi-cli/pull/1175) ([jwodder](https://github.com/jwodder))

Authors: 1

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

---

🚀 Enhancement

- Add validation of filepaths for non-BIDS NWB assets [1173](https://github.com/dandi/dandi-cli/pull/1173) ([jwodder](https://github.com/jwodder))
- Exclude special dotfiles from Zarrs [1147](https://github.com/dandi/dandi-cli/pull/1147) ([jwodder](https://github.com/jwodder))
- Structured validation results [1104](https://github.com/dandi/dandi-cli/pull/1104) ([jwodder](https://github.com/jwodder) [yarikoptic](https://github.com/yarikoptic) [TheChymera](https://github.com/TheChymera))

🐛 Bug Fix

- Allow user to specify mandatory (if not empty) fields in organize [1171](https://github.com/dandi/dandi-cli/pull/1171) ([yarikoptic](https://github.com/yarikoptic) [jwodder](https://github.com/jwodder))
- BF: convert str errors from checking nwb version into proper ValidationResult [1174](https://github.com/dandi/dandi-cli/pull/1174) ([yarikoptic](https://github.com/yarikoptic))
- Tests for `ls` reinstated, underlying function fixed, support for ZARR-BIDS files added. [1164](https://github.com/dandi/dandi-cli/pull/1164) ([TheChymera](https://github.com/TheChymera) [jwodder](https://github.com/jwodder))
- Add CodeQL workflow for GitHub code scanning and fix few bugs it detected [1165](https://github.com/dandi/dandi-cli/pull/1165) ([lgtm-migrator](https://github.com/lgtm-migrator) [jwodder](https://github.com/jwodder) [lgtm-com[bot]](https://github.com/lgtm-com[bot]))
- Corrected reporting function logic to complete group message variable [1166](https://github.com/dandi/dandi-cli/pull/1166) ([TheChymera](https://github.com/TheChymera))
- Renamed failing test, added prospective use case for NWBI warning. [1162](https://github.com/dandi/dandi-cli/pull/1162) ([TheChymera](https://github.com/TheChymera))
- Use cached namespace validation [1149](https://github.com/dandi/dandi-cli/pull/1149) ([CodyCBakerPhD](https://github.com/CodyCBakerPhD))

🏠 Internal

- Make `list_paths()` include dotfiles [1142](https://github.com/dandi/dandi-cli/pull/1142) ([jwodder](https://github.com/jwodder))

📝 Documentation

- dandi-cli readme edit [1170](https://github.com/dandi/dandi-cli/pull/1170) ([melster1010](https://github.com/melster1010))
- Remove Parameters description from docstring used by click [1150](https://github.com/dandi/dandi-cli/pull/1150) ([yarikoptic](https://github.com/yarikoptic))

🧪 Tests

- No longer mark `test_rename_type_mismatch` as xfailing [1161](https://github.com/dandi/dandi-cli/pull/1161) ([jwodder](https://github.com/jwodder))
- Fix typing error under mypy 0.990 [1156](https://github.com/dandi/dandi-cli/pull/1156) ([jwodder](https://github.com/jwodder))
- Update `test_validate_nwb_path_grouping` test [1157](https://github.com/dandi/dandi-cli/pull/1157) ([jwodder](https://github.com/jwodder))
- Fixed logic and commented a temporarily broken BIDS (lacking README) dataset [1148](https://github.com/dandi/dandi-cli/pull/1148) ([TheChymera](https://github.com/TheChymera))
- Installing hdf5 for Python 3.10 is no longer needed [1145](https://github.com/dandi/dandi-cli/pull/1145) ([jwodder](https://github.com/jwodder))
- Fix a typing issue involving the outdated `tmpdir_factory` [1144](https://github.com/dandi/dandi-cli/pull/1144) ([jwodder](https://github.com/jwodder))

Authors: 7

- [lgtm-com[bot]](https://github.com/lgtm-com[bot])
- Cody Baker ([CodyCBakerPhD](https://github.com/CodyCBakerPhD))
- Horea Christian ([TheChymera](https://github.com/TheChymera))
- John T. Wodder II ([jwodder](https://github.com/jwodder))
- LGTM Migrator ([lgtm-migrator](https://github.com/lgtm-migrator))
- Mary Elise Dedicke ([melster1010](https://github.com/melster1010))
- Yaroslav Halchenko ([yarikoptic](https://github.com/yarikoptic))

---

🐛 Bug Fix

- Don't try to cancel failed Zarr uploads twice [1139](https://github.com/dandi/dandi-cli/pull/1139) ([jwodder](https://github.com/jwodder))

📝 Documentation

- adding testing instructions [1123](https://github.com/dandi/dandi-cli/pull/1123) ([djarecka](https://github.com/djarecka))

🧪 Tests

- Add `DANDI_TESTS_PULL_DOCKER_COMPOSE` envvar [1141](https://github.com/dandi/dandi-cli/pull/1141) ([jwodder](https://github.com/jwodder))

Authors: 2

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

---