Dandi

🚀 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))

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🚀 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))

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🔩 Dependency Updates

- upgrade dandischema requirement from 0.4.1 to 0.5.1 (~=) [868](https://github.com/dandi/dandi-cli/pull/868) ([yarikoptic](https://github.com/yarikoptic))

Authors: 1

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

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🚀 Enhancement

- Include "dandiset" field in /uploads/initialize/ requests [863](https://github.com/dandi/dandi-cli/pull/863) ([jwodder](https://github.com/jwodder))

🐛 Bug Fix

- ENH: update species interpretation from NWB file [857](https://github.com/dandi/dandi-cli/pull/857) ([satra](https://github.com/satra))

Authors: 2

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

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🚀 Enhancement

- Add `embargo_status` to dandiset endpoint [855](https://github.com/dandi/dandi-cli/pull/855) ([dchiquito](https://github.com/dchiquito))
- Remove dandi/core/ in favor of copy in dandischema [849](https://github.com/dandi/dandi-cli/pull/849) ([jwodder](https://github.com/jwodder))
- Error on NWB files with external links [843](https://github.com/dandi/dandi-cli/pull/843) ([jwodder](https://github.com/jwodder))

🐛 Bug Fix

- Add DJANGO_DANDI_DANDISETS_EMBARGO_BUCKET_NAME setting to test docker-compose.yml [854](https://github.com/dandi/dandi-cli/pull/854) ([dchiquito](https://github.com/dchiquito))

🏠 Internal

- Move a comment [862](https://github.com/dandi/dandi-cli/pull/862) ([jwodder](https://github.com/jwodder))
- Add a wrapper function for the calls to `find_files()` in tests [860](https://github.com/dandi/dandi-cli/pull/860) ([jwodder](https://github.com/jwodder))
- Assorted code cleanups [859](https://github.com/dandi/dandi-cli/pull/859) ([jwodder](https://github.com/jwodder))
- Remove generatorify.py [850](https://github.com/dandi/dandi-cli/pull/850) ([jwodder](https://github.com/jwodder))

📝 Documentation

- Improve CLI documentation [851](https://github.com/dandi/dandi-cli/pull/851) ([jwodder](https://github.com/jwodder))

🧪 Tests

- Replace the use of pyfakefs with a `tmp_home` fixture [861](https://github.com/dandi/dandi-cli/pull/861) ([jwodder](https://github.com/jwodder))

Authors: 2

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

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🐛 Bug Fix

- Improve UX of failed redirects while resolving resource identifiers [830](https://github.com/dandi/dandi-cli/pull/830) ([jwodder](https://github.com/jwodder))

🏠 Internal

- Remove some unused functions [846](https://github.com/dandi/dandi-cli/pull/846) ([jwodder](https://github.com/jwodder))

🧪 Tests

- Set new environment variables required by API server [845](https://github.com/dandi/dandi-cli/pull/845) ([mvandenburgh](https://github.com/mvandenburgh))
- Test against Python 3.10 [794](https://github.com/dandi/dandi-cli/pull/794) ([jwodder](https://github.com/jwodder))
- Ignore a deprecation warning from humanize [844](https://github.com/dandi/dandi-cli/pull/844) ([jwodder](https://github.com/jwodder))

Authors: 2

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

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