Dandi

🚀 Enhancement

- Refactor some download code for readability + ensure that we checksum resumed downloads [1535](https://github.com/dandi/dandi-cli/pull/1535) ([yarikoptic](https://github.com/yarikoptic))

🐛 Bug Fix

- Fix `PrivateAttr` usage [1538](https://github.com/dandi/dandi-cli/pull/1538) ([jwodder](https://github.com/jwodder))
- add one photon to metadata dict [1532](https://github.com/dandi/dandi-cli/pull/1532) ([bendichter](https://github.com/bendichter))

🧪 Tests

- Ignore some type-checking errors under Python 3.13 [1539](https://github.com/dandi/dandi-cli/pull/1539) ([jwodder](https://github.com/jwodder))
- tests: update tests docker-compose with few changes from dandi-archive [1531](https://github.com/dandi/dandi-cli/pull/1531) ([yarikoptic](https://github.com/yarikoptic))
- Specify custom ulimit on nofiles to prevent infinite loop by billiard [1533](https://github.com/dandi/dandi-cli/pull/1533) ([yarikoptic](https://github.com/yarikoptic))
- Rename `file` key to codecov-action to `files` [1530](https://github.com/dandi/dandi-cli/pull/1530) ([jwodder](https://github.com/jwodder))
- [gh-actions](deps): Bump codecov/codecov-action from 4 to 5 [1529](https://github.com/dandi/dandi-cli/pull/1529) ([dependabot[bot]](https://github.com/dependabot[bot]))

Authors: 4

- [dependabot[bot]](https://github.com/dependabot[bot])
- Ben Dichter ([bendichter](https://github.com/bendichter))
- John T. Wodder II ([jwodder](https://github.com/jwodder))
- Yaroslav Halchenko ([yarikoptic](https://github.com/yarikoptic))

---

🚀 Enhancement

- download: more consistent and exhaustive logging, new `DANDI_DEVEL_AGGRESSIVE_RETRY` mode, respect (?) Retry-After [1509](https://github.com/dandi/dandi-cli/pull/1509) ([yarikoptic](https://github.com/yarikoptic))

🐛 Bug Fix

- Include LINC API as a supported instance type for DANDI CLI [1527](https://github.com/dandi/dandi-cli/pull/1527) (aaronkanzerAarons-MacBook-Pro.local [aaronkanzer](https://github.com/aaronkanzer))
- Enhance pynwb validation parsing to report the path within the file, fix pynwb typo [1513](https://github.com/dandi/dandi-cli/pull/1513) ([rly](https://github.com/rly))
- Drop claiming support and testing against EOL Python 3.8 [1504](https://github.com/dandi/dandi-cli/pull/1504) ([asmacdo](https://github.com/asmacdo))
- ENH: log dandischema version and ensure we log (consistently) path for log messages in download [1499](https://github.com/dandi/dandi-cli/pull/1499) ([yarikoptic](https://github.com/yarikoptic))
- Fixup URI scheme rendering in --help output [1502](https://github.com/dandi/dandi-cli/pull/1502) ([asmacdo](https://github.com/asmacdo))
- Adjust copyright year in documentation config [1504](https://github.com/dandi/dandi-cli/pull/1504) ([yarikoptic](https://github.com/yarikoptic))

🏠 Internal

- Use "cache_spec:False" in our copy_nwb_file helper while exporting NWB copy [1497](https://github.com/dandi/dandi-cli/pull/1497) ([yarikoptic](https://github.com/yarikoptic))

📝 Documentation

- fix: replace dandi-api link with dandi-archive [1524](https://github.com/dandi/dandi-cli/pull/1524) ([asmacdo](https://github.com/asmacdo))

🧪 Tests

- Add xfail marks for some tests: test_nwb2asset_remote_asset, test_reextract_metadata, test_IteratorWithAggregation [1512](https://github.com/dandi/dandi-cli/pull/1512) ([yarikoptic](https://github.com/yarikoptic))
- Switch to python 3.9 in dev-deps CI matrix run since dev deps are now beginning to drop Python 3.8 which is EOL soon [1506](https://github.com/dandi/dandi-cli/pull/1506) ([asmacdo](https://github.com/asmacdo))

Authors: 5

- [aaronkanzer](https://github.com/aaronkanzer)
- Aaron Kanzer (aaronkanzerAarons-MacBook-Pro.local)
- Austin Macdonald ([asmacdo](https://github.com/asmacdo))
- Ryan Ly ([rly](https://github.com/rly))
- Yaroslav Halchenko ([yarikoptic](https://github.com/yarikoptic))

---

🐛 Bug Fix

- Disallow hdmf 3.14.4, make organize to not parallelize for a single file, log information about all exceptions while reading metadata for organize [1496](https://github.com/dandi/dandi-cli/pull/1496) ([yarikoptic](https://github.com/yarikoptic))
- BF: use correct variable in exception upon unknown how to handle value of "species" [1482](https://github.com/dandi/dandi-cli/pull/1482) ([yarikoptic](https://github.com/yarikoptic))
- move: Immediately authenticate client after creation [1480](https://github.com/dandi/dandi-cli/pull/1480) ([jwodder](https://github.com/jwodder))

🧪 Tests

- Dump audit table to file specified by `DANDI_TESTS_AUDIT_CSV` envvar [1486](https://github.com/dandi/dandi-cli/pull/1486) ([jwodder](https://github.com/jwodder))
- Fix host used in minio URLs [1487](https://github.com/dandi/dandi-cli/pull/1487) ([jwodder](https://github.com/jwodder))

Authors: 2

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

---

🚀 Enhancement

- Add `--preserve-tree` option to `dandi download` [1467](https://github.com/dandi/dandi-cli/pull/1467) ([jwodder](https://github.com/jwodder))

🐛 Bug Fix

- Fix handling of `--preserve-tree` for asset ID-only URLs [1476](https://github.com/dandi/dandi-cli/pull/1476) ([jwodder](https://github.com/jwodder))

📝 Documentation

- Fix one insignificant typo in CHANGELOG [1477](https://github.com/dandi/dandi-cli/pull/1477) ([yarikoptic](https://github.com/yarikoptic))

🧪 Tests

- Revert "Unbreak vcrpy install" [1472](https://github.com/dandi/dandi-cli/pull/1472) ([jwodder](https://github.com/jwodder))
- Unbreak vcrpy install [1471](https://github.com/dandi/dandi-cli/pull/1471) ([jwodder](https://github.com/jwodder))
- Further improvements to `docker-compose.yml` [1470](https://github.com/dandi/dandi-cli/pull/1470) ([jwodder](https://github.com/jwodder))
- Assorted Docker Compose improvements [1465](https://github.com/dandi/dandi-cli/pull/1465) ([jwodder](https://github.com/jwodder))
- Do not use mypy 1.11.0 [1466](https://github.com/dandi/dandi-cli/pull/1466) ([jwodder](https://github.com/jwodder))

Authors: 2

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

---

🔩 Dependency Updates

- Revert "Temporarily restrict dandischema requirement to `< 0.10.2`" [1459](https://github.com/dandi/dandi-cli/pull/1459) ([jwodder](https://github.com/jwodder))

Authors: 1

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

---

🔩 Dependency Updates

- Temporarily restrict dandischema requirement to `< 0.10.2` [1458](https://github.com/dandi/dandi-cli/pull/1458) ([jwodder](https://github.com/jwodder))

Authors: 1

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

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