Webknossos

webknossos

Breaking Changes
- `Dataset.upload()` now returns a `RemoteDataset` instead instead of the URL string. You can get the URL via `remote_ds.url`. [723](https://github.com/scalableminds/webknossos-libs/pull/723)
- `User.teams` now is a tuple instead of a list. [723](https://github.com/scalableminds/webknossos-libs/pull/723)
- The deprecated `download_dataset` function now requires the `organization_id` argument. [723](https://github.com/scalableminds/webknossos-libs/pull/723)

Added
- Added `Dataset.open_remote()`, which returns an object of the new `RemoteDataset`. [723](https://github.com/scalableminds/webknossos-libs/pull/723)
This can
* give the webknossos URL for the dataset as `remote_ds.url`,
* read image data via the webknossos zarr interface, using the inherited `Dataset` methods, and
* read and change the following dataset metadata as properties: `display_name`, `description`, `tags`, `is_public`, `sharing_token`, `allowed_teams`.
- `Team` instances also contain the `organization_id`. [723](https://github.com/scalableminds/webknossos-libs/pull/723)

webknossos

Fixed
- Fixed upsampling with constant z in certain anisotropic cases. [720](https://github.com/scalableminds/webknossos-libs/pull/720)

webknossos

Breaking Changes
- Renamed some entities to comply with the [webKnossos terminology](https://docs.webknossos.org/webknossos/terminology.html). [#704](https://github.com/scalableminds/webknossos-libs/pull/704):
* The `Graph` class changed to `Tree`, also related methods and attributes are renamed now, e.g. `add_graph` is now `add_tree`.
All previous entities are still available, but deprecated.
* `scale` has changed to `voxel_size` for datasets, skeletons and annotations.
Changes in `Dataset` are backwards-compatible, but `scale` is deprecated.
For `Annotation` and `Skeletons` the initializer only supports `voxel_size`, the `scale` attribute is deprecated
* `get_best_mag` is deprecated, please use `get_finest_mag` instead
* In `layer.upscale`, `min_mag` is deprecated in favor of `finest_mag`

Fixed
- Correctly maintain default_view_configuration property when downloading a dataset. [677](https://github.com/scalableminds/webknossos-libs/pull/677)


wkcuber

Breaking Changes
- Deprecated `--scale` in favor of `--voxel_size`. [704](https://github.com/scalableminds/webknossos-libs/pull/704)

Fixed
- Fixed a bug where upper-case file extensions would lead to errors during channel count detection. [709](https://github.com/scalableminds/webknossos-libs/pull/709)

webknossos

Fixed

- Fixed a bug where the server’s error message during dataset upload was not displayed to the user. [702](https://github.com/scalableminds/webknossos-libs/pull/702)


wkcuber

Breaking Changes
- Deprecated `--wkw_file_len` flags in favor of `--chunks_per_shard`. [679](https://github.com/scalableminds/webknossos-libs/pull/679)
- Deprecated `wkcuber.api` in favor of the high-level `webknososs.Dataset` API. [679](https://github.com/scalableminds/webknossos-libs/pull/679)
- Deprecated external use of `wkcuber.utils`. [679](https://github.com/scalableminds/webknossos-libs/pull/679)
- Remove the deprecated modules `wkcuber.downsampling_utils` and `wkcuber.upsampling_utils`. Use the high-level `Layer.downsample` and `Layer.upsample` methods in the `webknossos` package instead. [679](https://github.com/scalableminds/webknossos-libs/pull/679)

Added
- Added Zarr support for `wkcuber`, `wkcuber.cubing`, `wkcuber.converter`, `wkcuber.convert_knossos`, `wkcuber.convert_image_stack_to_wkw`, `wkcuber.convert_nifti`, `wkcuber.convert_raw`, `wkcuber.convert_zarr`, and `wkcuber.recubing`. These commands now take a `--data_format` flag that can either be `wkw` or `zarr`. Additionally, `--chunk_size` and `--chunks_per_shard` flag are available and take either a single number or a 3-tuple (e.g. `32,32,32`). [689](https://github.com/scalableminds/webknossos-libs/pull/679)