Webknossos

webknossos

Breaking Changes
- Task/Project management: `open` tasks have been renamed to `pending`. Use `Task.status.pending_instance_count` instead of `Task.status.open_instance_count`. [930](https://github.com/scalableminds/webknossos-libs/pull/930)

Fixed
- Fixed an infinite loop in the mag calculation during anisotropic downsampling in situations where the target mag cannot possibly be reached while adhering to the anisotropic downsampling scheme. [934](https://github.com/scalableminds/webknossos-libs/pull/934)

webknossos

Added
- `View` has a `map_chunk` method now to run a function on each chunk and collect the results in a list.

Changed
- As WEBKNOSSOS does not require the largest segment id. It is also not mandatory in the WEBKNOSSOS libs anymore. [917](https://github.com/scalableminds/webknossos-libs/issues/917) The method `SegmentationLayer.refresh_largest_segment_id` was added to lookup the highest value in segmentation data and set `largest_segment_id` accordingly.
- The `convert` command of the cli now has a `--category` flag, to select the LayerCategoryType.

webknossos

Changed
- The `convert` command of the cli now has a `--category` flag, to select the LayerCategoryType.


cluster_tools

Added
- From now on the cluster tools will detect if slurm jobs were killed, because they exceeded the configured time limit, and throw a `RemoteTimeLimitException` indicating the issue instead of a generic `RemoteException`. If it is unclear whether a job was killed because of the time or memory limit, a `RemoteResourceLimitException` is thrown. [929](https://github.com/scalableminds/webknossos-libs/pull/929)

webknossos

Changed
- The conversion folder structures to layer names does not allow slashes in the layer name anymore. [918](https://github.com/scalableminds/webknossos-libs/issues/918)

Fixed
- Fixed a bug where compression in add_layer_from_images uses too much memory [900](https://github.com/scalableminds/webknossos-libs/issues/900)

webknossos

Added
- Added `duration_in_seconds` and `modified` to `AnnotationInfo`. [914](https://github.com/scalableminds/webknossos-libs/pull/914)
- Added [`zarrita`](https://github.com/scalableminds/zarrita) storage backend for arrays. zarrita supports Zarr v2 and v3 including sharding. To activate zarrita, the environment variable `WK_USE_ZARRITA` must be set. [#912](https://github.com/scalableminds/webknossos-libs/pull/912)
- Added a `Zarr3` data format which supports sharding. [912](https://github.com/scalableminds/webknossos-libs/pull/912)

Changed
- Integrated the `wkcuber` CLI tool into `webknossos` package. [903](https://github.com/scalableminds/webknossos-libs/pull/903)
- To get an overview of all webknossos subcommands type `webknossos --help`. If the usage of a single subcommand is of interest type `webknossos <subcommand> --help`
- These commands were changed:
- `python -m wkcuber`, `python -m wkcuber.convert_image_stack_to_wkw` -> `webknossos convert`
- `python -m wkcuber.export_wkw_as_tiff` -> `webknossos export-wkw-as-tiff`
- `python -m wkcuber.convert_knossos` -> `webknossos convert-knossos`
- `python -m wkcuber.convert_nifti` -> `webknossos convert-nifti`
- `python -m wkcuber.convert_raw` -> `webknossos convert-raw`
- `python -m wkcuber.downsampling` -> `webknossos downsample`
- `python -m wkcuber.compress` -> `webknossos compress`
- `python -m wkcuber.check_equality` -> `webknossos check-equality`
- There is one new command:
- `webknossos upload` to upload a dataset to a WEBKNOSSOS server
- These commands have been removed:
- `python -m wkcuber.cubing`
- `python -m wkcuber.tile_cubing`
- `python -m wkcuber.metadata`
- `python -m wkcuber.recubing`

Fixed
- Fixed a bug where upsampling of a layer would fail, if the layer had a bounding box that doesn't align with the from_mag mag. [915](https://github.com/scalableminds/webknossos-libs/pull/915)

wkcuber
The `wkcuber` package is now deprecated because the CLI was integrated into the `webknossos` package. Please use the CLI in the `webknossos` package instead.

webknossos

Changed
- Upgrades `wkw`. [911](https://github.com/scalableminds/webknossos-libs/pull/911)