Webknossos

webknossos

Added
- Added `list_bounding_boxes()` for Zarr-based datasets. [1238](https://github.com/scalableminds/webknossos-libs/pull/1238)

webknossos

Breaking Changes
- `RemoteDataset.display_name` is deprecated. To change the name of a dataset use the `name` property instead.
- `Dataset.get_remote_datasets()` returns a mapping. The keys of this mapping changed from datasets name to datasets id.
- `Task.create()` needs a `dataset_id` now instead of a `dataset_name`. Alternativly a `RemoteDataset` object can be used. The `dataset_name` is marked as deprecated. As `dataset_name` is an optional argument now its position has changed, this is important if `create()` is called only with positional arguments.
- When uploading an Annotation the organization_id is neccessary now. The organization_id might be stored in the Annotation object or it is inferred from the current webknossos_context. [1155](https://github.com/scalableminds/webknossos-libs/pull/1155)

Added
- `Dataset` method `get_remote_datasets()` accepts `name` and `folder_id` as arguments now to filter remote datasets.
- `RemoteDataset` got an additional property: `created`.
- `Annotation` got an additional property: `dataset_id`.
- `Dataset.trigger_dataset_import()` was added to refresh the datastore to register a newly added dataset. [1236](https://github.com/scalableminds/webknossos-libs/pull/1236)

Changed
- Updated to WEBKNOSSOS API version 9. This includes support for the new url structure for datasets and the usage of `dataset_id`. [1231](https://github.com/scalableminds/webknossos-libs/pull/1231)

Fixed
- Fixed Mag setup for non-public datasets. [1222](https://github.com/scalableminds/webknossos-libs/pull/1222)
- Fixed an issue when shallow copying datasets with a remote mag. [1224](https://github.com/scalableminds/webknossos-libs/pull/1224)

webknossos

Breaking Changes
- `MagView.get_zarr_array` now returns a `tensorstore` array instead of a `zarr-python` array. [1174](https://github.com/scalableminds/webknossos-libs/pull/1174)

Changed
- Updated to WEBKNOSSOS API version 8. [1185](https://github.com/scalableminds/webknossos-libs/pull/1185)
- Using tensorstore for reading and writing zarr 2 and 3 arrays. Removed `zarrita` and `zarr` dependency. [1174](https://github.com/scalableminds/webknossos-libs/pull/1174)

webknossos

Added
- Added .nrrd and .nhdr to supported suffixes. [1228](https://github.com/scalableminds/webknossos-libs/pull/1228)
- Added more docstrings for many public classes and methods. [1225](https://github.com/scalableminds/webknossos-libs/pull/1225)

Changed
- Removes vcr-py from developer dependencies for testing and adds proxay for recording and replaying API requests. [1198](https://github.com/scalableminds/webknossos-libs/pull/1198)
- Removed the CZI installation extra from `pip install webknossos[all]` by default. Users need to manually install it with `pip install --extra-index-url https://pypi.scm.io/simple/ webknossos[czi]`. [#1219](https://github.com/scalableminds/webknossos-libs/pull/1219)
- Refactored the PimsTiffReader to read the data directly from the tiff file without creating a memmap-able copy first. This greatly reduces the time and storage requirements for converting large tiff files. [1212](https://github.com/scalableminds/webknossos-libs/pull/1212)

Fixed
- Fixed unpickling of the SSL_Context to allow for a second or third pickling. [1223](https://github.com/scalableminds/webknossos-libs/pull/1223)

cluster_tools

Breaking Changes
- Removed the `map_unordered` function of executors. [1193](https://github.com/scalableminds/webknossos-libs/pull/1193)

Changed
- Deprecated the test_pickling and debug_sequential executor strategies. The strategies multiprocessing_with_pickling and sequential should be used instead. [1193](https://github.com/scalableminds/webknossos-libs/pull/1193)
- The sequential executor strategy no longer uses multiprocessing functionality internally and instead executes functions sequentially and synchronously in the same process. [1193](https://github.com/scalableminds/webknossos-libs/pull/1193)

webknossos

Fixed
- Fixed pickling issue that has been introduced in 0.15.9. [1218](https://github.com/scalableminds/webknossos-libs/pull/1218)