Dandi

🐛 Bug Fix

- Fix type in test docker-compose env var [960](https://github.com/dandi/dandi-cli/pull/960) ([AlmightyYakob](https://github.com/AlmightyYakob))

Authors: 1

- Jacob Nesbitt ([AlmightyYakob](https://github.com/AlmightyYakob))

---

🚀 Enhancement

- Add DANDI_JUPYTERHUB_URL to test docker-compose [959](https://github.com/dandi/dandi-cli/pull/959) ([AlmightyYakob](https://github.com/AlmightyYakob))
- Integrate NWBInspector with DANDI validation [941](https://github.com/dandi/dandi-cli/pull/941) ([CodyCBakerPhD](https://github.com/CodyCBakerPhD))

🐛 Bug Fix

- Integration test config [957](https://github.com/dandi/dandi-cli/pull/957) ([dchiquito](https://github.com/dchiquito))
- Smaller video files [947](https://github.com/dandi/dandi-cli/pull/947) ([TheChymera](https://github.com/TheChymera))

⚠️ Pushed to `master`

- add .mkv as a valid video extension ([bendichter](https://github.com/bendichter))

🏠 Internal

- DX: enable "released" plugin for auto [951](https://github.com/dandi/dandi-cli/pull/951) ([yarikoptic](https://github.com/yarikoptic))

🧪 Tests

- Fixed test_write_report() log path issue [954](https://github.com/dandi/dandi-cli/pull/954) ([TheChymera](https://github.com/TheChymera))
- Specify all queues in test celery worker [953](https://github.com/dandi/dandi-cli/pull/953) ([dchiquito](https://github.com/dchiquito))
- Work around a bug in docker-compose [949](https://github.com/dandi/dandi-cli/pull/949) ([jwodder](https://github.com/jwodder))

Authors: 7

- Ben Dichter ([bendichter](https://github.com/bendichter))
- Cody Baker ([CodyCBakerPhD](https://github.com/CodyCBakerPhD))
- Daniel Chiquito ([dchiquito](https://github.com/dchiquito))
- Horea Christian ([TheChymera](https://github.com/TheChymera))
- Jacob Nesbitt ([AlmightyYakob](https://github.com/AlmightyYakob))
- John T. Wodder II ([jwodder](https://github.com/jwodder))
- Yaroslav Halchenko ([yarikoptic](https://github.com/yarikoptic))

---

🚀 Enhancement

- Adding BIDS support [896](https://github.com/dandi/dandi-cli/pull/896) ([yarikoptic](https://github.com/yarikoptic) [TheChymera](https://github.com/TheChymera))

🏠 Internal

- Black update [945](https://github.com/dandi/dandi-cli/pull/945) ([TheChymera](https://github.com/TheChymera))

Authors: 2

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

---

🚀 Enhancement

- Recognize video files as non-generic assets [922](https://github.com/dandi/dandi-cli/pull/922) ([jwodder](https://github.com/jwodder))

🐛 Bug Fix

- Update for change in Zarr checksum format [933](https://github.com/dandi/dandi-cli/pull/933) ([jwodder](https://github.com/jwodder))
- Trigger Zarr ingestion after performing an upload [938](https://github.com/dandi/dandi-cli/pull/938) ([jwodder](https://github.com/jwodder))
- check for existence of video path else assume relative path [931](https://github.com/dandi/dandi-cli/pull/931) ([Saksham20](https://github.com/Saksham20))
- dandi upload: Make `--jobs` default to `5:5` and document it [940](https://github.com/dandi/dandi-cli/pull/940) ([jwodder](https://github.com/jwodder))
- checking for duplicate video files in external_files [928](https://github.com/dandi/dandi-cli/pull/928) ([Saksham20](https://github.com/Saksham20))
- skip handling URLs in external files references as we do for local paths [932](https://github.com/dandi/dandi-cli/pull/932) ([Saksham20](https://github.com/Saksham20))
- Let `dandi delete` take paths to local Zarrs [925](https://github.com/dandi/dandi-cli/pull/925) ([jwodder](https://github.com/jwodder))

🏎 Performance

- Minimize/optimize Zarr digestion when uploading [923](https://github.com/dandi/dandi-cli/pull/923) ([jwodder](https://github.com/jwodder))
- Don't repeat API requests when finding subdir files to delete before Zarr upload [919](https://github.com/dandi/dandi-cli/pull/919) ([jwodder](https://github.com/jwodder))

📝 Documentation

- Correct the docstring for `BasePath.parents` [936](https://github.com/dandi/dandi-cli/pull/936) ([jwodder](https://github.com/jwodder))

Authors: 2

- John T. Wodder II ([jwodder](https://github.com/jwodder))
- Saksham Sharda ([Saksham20](https://github.com/Saksham20))

---

🚀 Enhancement

- Add zarr-checksum method to `dandi digest` [900](https://github.com/dandi/dandi-cli/pull/900) ([jwodder](https://github.com/jwodder))
- Move `dandi organize` code to an `organize()` function [902](https://github.com/dandi/dandi-cli/pull/902) ([jwodder](https://github.com/jwodder))
- Video files organize [841](https://github.com/dandi/dandi-cli/pull/841) ([Saksham20](https://github.com/Saksham20))
- Make use of `/assets/{asset_id}/info/` endpoint [895](https://github.com/dandi/dandi-cli/pull/895) ([jwodder](https://github.com/jwodder))
- Support Zarr directories [853](https://github.com/dandi/dandi-cli/pull/853) ([jwodder](https://github.com/jwodder))

🐛 Bug Fix

- Make `dandi upload` look for dandiset.yaml in parents of common path [916](https://github.com/dandi/dandi-cli/pull/916) ([jwodder](https://github.com/jwodder))
- Mint Zarr assets at start of upload and sync Zarr contents [907](https://github.com/dandi/dandi-cli/pull/907) ([jwodder](https://github.com/jwodder))
- Use full asset path as name of Zarr object [912](https://github.com/dandi/dandi-cli/pull/912) ([jwodder](https://github.com/jwodder))
- Specify Dandiset ID when creating a Zarr [911](https://github.com/dandi/dandi-cli/pull/911) ([jwodder](https://github.com/jwodder))
- Cancel a Zarr upload if an error occurs partway through [893](https://github.com/dandi/dandi-cli/pull/893) ([jwodder](https://github.com/jwodder))
- Make `get_raw_digest()` actually default to the proper digest type for Zarrs [894](https://github.com/dandi/dandi-cli/pull/894) ([jwodder](https://github.com/jwodder))
- Fix neural data type to metadata extractor [891](https://github.com/dandi/dandi-cli/pull/891) ([satra](https://github.com/satra) [yarikoptic](https://github.com/yarikoptic))

🏠 Internal

- Add dedicated HTTP404Error exception class [908](https://github.com/dandi/dandi-cli/pull/908) ([jwodder](https://github.com/jwodder))
- Make `paths` argument to `upload()` optional [899](https://github.com/dandi/dandi-cli/pull/899) ([jwodder](https://github.com/jwodder))
- Add type-annotations to various files [887](https://github.com/dandi/dandi-cli/pull/887) ([jwodder](https://github.com/jwodder))
- Delete functions (get_asset_metadata, find_dandi_files) obsoleted by PR 853 [885](https://github.com/dandi/dandi-cli/pull/885) ([jwodder](https://github.com/jwodder))
- Use a pydantic model to store a RemoteDandiset's cached data [876](https://github.com/dandi/dandi-cli/pull/876) ([jwodder](https://github.com/jwodder))

📝 Documentation

- improve DandiApiClient.__init__ docstring [909](https://github.com/dandi/dandi-cli/pull/909) ([bendichter](https://github.com/bendichter))
- Document new `dandi organize` options in Read the Docs site [901](https://github.com/dandi/dandi-cli/pull/901) ([jwodder](https://github.com/jwodder))
- Organize & fine-tune dandi.dandiapi Sphinx docs [888](https://github.com/dandi/dandi-cli/pull/888) ([jwodder](https://github.com/jwodder))

🧪 Tests

- Pin minio image version [898](https://github.com/dandi/dandi-cli/pull/898) ([AlmightyYakob](https://github.com/AlmightyYakob))
- Enable type-checking [877](https://github.com/dandi/dandi-cli/pull/877) ([jwodder](https://github.com/jwodder))
- Add `new_dandiset` fixture [874](https://github.com/dandi/dandi-cli/pull/874) ([jwodder](https://github.com/jwodder))
- Mark a test with missing `skipif_no_network` marker [886](https://github.com/dandi/dandi-cli/pull/886) ([jwodder](https://github.com/jwodder))

🔩 Dependency Updates

- Remove unused tqdm dependency [910](https://github.com/dandi/dandi-cli/pull/910) ([jwodder](https://github.com/jwodder))
- Update minimum pydantic version to 1.9.0 [905](https://github.com/dandi/dandi-cli/pull/905) ([jwodder](https://github.com/jwodder))

Authors: 6

- Ben Dichter ([bendichter](https://github.com/bendichter))
- Jacob Nesbitt ([AlmightyYakob](https://github.com/AlmightyYakob))
- John T. Wodder II ([jwodder](https://github.com/jwodder))
- Saksham Sharda ([Saksham20](https://github.com/Saksham20))
- Satrajit Ghosh ([satra](https://github.com/satra))
- Yaroslav Halchenko ([yarikoptic](https://github.com/yarikoptic))

---

🚀 Enhancement

- Make navigate() and navigate_url() auto-authenticate for embargoed Dandisets [870](https://github.com/dandi/dandi-cli/pull/870) ([jwodder](https://github.com/jwodder))

🐛 Bug Fix

- species url is case sensitive [865](https://github.com/dandi/dandi-cli/pull/865) ([jwodder](https://github.com/jwodder) [satra](https://github.com/satra))

🏠 Internal

- Update bad versions list in `.et` [866](https://github.com/dandi/dandi-cli/pull/866) ([jwodder](https://github.com/jwodder))

Authors: 2

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

---