Webknossos

webknossos

Breaking Changes
- The `Annotation` constructor takes the `owner_name` argument instead of `username`. This is only important when using keyword arguments. The `username` attributes are still available as a proxy for the `owner_name` attribute, but deprecated. [760](https://github.com/scalableminds/webknossos-libs/pull/760)
- `user_id` on `AnnotationInfo` objects is deprecated, please use `owner_id` instead. [760](https://github.com/scalableminds/webknossos-libs/pull/760)
- When self-hosting a webKnossos server, please note that a webknossos version >= `22.06.0` is required. [760](https://github.com/scalableminds/webknossos-libs/pull/760) & [#764](https://github.com/scalableminds/webknossos-libs/pull/764)

Added
- `Dataset.upload()` accepts `Layer` objects from a `RemoteDataset` in the `layers_to_link` argument list. Also, `LayerToLink` can consume those via `LayerToLink.from_remote_layer()`. [761](https://github.com/scalableminds/webknossos-libs/pull/761)
- `Task.create()` accepts a `RemoteDataset` for the `dataset_name` argument. [761](https://github.com/scalableminds/webknossos-libs/pull/761)
- Added `annotation.get_remote_base_dataset()` returning a `RemoteDataset`. [761](https://github.com/scalableminds/webknossos-libs/pull/761)
- Added `Team.get_by_name()`. [763](https://github.com/scalableminds/webknossos-libs/pull/763)
- Added `Dataset.get_remote_datasets()`. [763](https://github.com/scalableminds/webknossos-libs/pull/763)

Changed
- If a token is requested from the user on the commandline, it is now stored in the current context. Before, it was discarded. [761](https://github.com/scalableminds/webknossos-libs/pull/761)
- `Annotation.download()` does not need the `annotation_type` anymore, and the type can also be omitted from passed URLs. [764](https://github.com/scalableminds/webknossos-libs/pull/764)
- `Dataset.add_layer_from_images` allows smaller batch sizes for uncompressed writes. [766](https://github.com/scalableminds/webknossos-libs/pull/766)
- `Dataset.add_layer_from_images` uses multiprocessing by default. [766](https://github.com/scalableminds/webknossos-libs/pull/766)

Fixed
- Fixed the bounding box inferral for volume annotation layers that were not saved in Mag(1). [765](https://github.com/scalableminds/webknossos-libs/pull/765)


wkcuber

Changed
- Made the dataset upload more robust against network errors. [757](https://github.com/scalableminds/webknossos-libs/pull/757)

wkcuber

Changed
- Make KNOSSOS conversion compatible with mag-prefixed mag folders. [756](https://github.com/scalableminds/webknossos-libs/pull/756)
- When using multiprocessing, warning filters are set up to behave as in the
spawning context. [741](https://github.com/scalableminds/webknossos-libs/pull/741)

Fixed
- Fixed broken KNOSSOS to wkw conversion. [756](https://github.com/scalableminds/webknossos-libs/pull/756)

webknossos

Added
- Added export of [OME-NGFF v0.4 metadata](https://ngff.openmicroscopy.org/0.4/) for all `Dataset`s that have a Zarr layer [#737](https://github.com/scalableminds/webknossos-libs/pull/737)


wkcuber

Fixed
- Fixed a bug where nifti datasets would not be converted if called from the CLI. [733](https://github.com/scalableminds/webknossos-libs/pull/733)


cluster_tools

Added
- Detect when slurm jobs crash due to being out-of-memory. [739](https://github.com/scalableminds/webknossos-libs/pull/739)

webknossos

Changed
- added Python 3.9 support to wk-libs [716](https://github.com/scalableminds/webknossos-libs/pull/716)

Fixed
- URLs for the webknossos-context (e.g. in the `WK_URL` env var or via `webknossos_context(url=…)`) may now contain `/` in the end and are sanitized. Before, requests would fail if the URL contained a final `/`. [733](https://github.com/scalableminds/webknossos-libs/pull/733)


wkcuber

Changed
- Added Python 3.9 support to wkcuber [716](https://github.com/scalableminds/webknossos-libs/pull/716)


cluster_tools

Fixed
- Fix `_log() got unexpected keyword argument: 'file'` error for newer Python versions. [735](https://github.com/scalableminds/webknossos-libs/pull/735)